I found that it was definitely a rendering issue, not a SOQL issue.  The constant rerendering of a DataTable with 1000 or so records was causing very slow ajax rerendering.

I was able to solve the problem through the suggestion of the dynamic query, as well as adding some pagination by using the OFFSET in my SOQL.  I was able to do this rather easily using this great blog post from RedPointSolutions

http://blog.redpointsolutions.com/bid/182738/Add-Pagination-to-your-Visualforce-Pages-using-the-SOQL-OFFSET-Clause

Heres the final code if anyone might be interested

VF

<apex:page controller="testController">

<apex:sectionHeader title="Insurance Profile Campaign" subtitle="Master List"/>
    <apex:form >
    <apex:outputpanel id="container">
    <apex:outputpanel id="table">   
    <apex:pageblock >
    <apex:pageBlockButtons location="top">
        <apex:commandLink action="{!viewAll}" value="View All Unassigned" styleClass="btn" style="text-decoration:none" id="all" rerender="container,table"/>
        <apex:commandLink action="{!viewMine}" value="View Mine (Open)" styleClass="btn" style="text-decoration:none" id="viewMine" rerender="container,table"/>
        <apex:commandLink action="{!viewOthers}" value="View Others (Open)" styleClass="btn" style="text-decoration:none" id="others" rerender="container,table"/>
        <apex:commandLink action="{!viewMyCompleted}" value="View Mine (Completed)" styleClass="btn" style="text-decoration:none" id="myComp" rerender="container,table"/>
        <apex:commandLink action="{!viewOtherCompleted}" value="View Others (Completed)" styleClass="btn" style="text-decoration:none" id="otherComp" rerender="container,table"/>    
    </apex:pageBlockButtons>
    </apex:pageblock>
    <apex:pageblock tabStyle="Account">
    <apex:pageBlockButtons location="top" >
    <apex:outputPanel id="myButtons">
   
        <apex:commandButton action="{!Beginning}" title="Beginning" value="<<" style="width:35px;" disabled="{!disablePrevious}" reRender="myPanel,myButtons"/>
        <apex:commandButton action="{!Previous}" title="Previous" value="<" style="width:25px;" disabled="{!disablePrevious}" reRender="myPanel,myButtons"/>        
        <apex:commandButton action="{!Next}" title="Next" value=">" style="width:25px;" disabled="{!disableNext}" reRender="myPanel,myButtons"/>
        <apex:commandButton action="{!End}" title="End" value=">>" style="width:35px;" disabled="{!disableNext}" reRender="myPanel,myButtons"/>        
   
    </apex:outputPanel>
    </apex:pageBlockButtons>
    
    
    <apex:outputpanel id="myPanel">
    <apex:pageBlockSection title="{!listTitle}({!totalSize})" collapsible="false" columns="1">
    <apex:pageBlockTable value="{!results2}" var="pro" style="width:100%; border:1px solid #D4DADC;">
         
        <apex:column style="width:120px; padding-top:10px; padding-bottom:10px; text-align:center;" rendered="{!Filter == 'Show All'}">
            <apex:commandLink action="{!takeOwnership}" value="Take Ownership" styleClass="btn" style="text-decoration:none" rerender="table">
                <apex:param name="proId" value="{!pro.id}" />                          
            </apex:commandLink>
        </apex:column>
         
        <apex:column style="width:120px; padding-top:10px; padding-bottom:10px; text-align:center;" rendered="{!Filter != 'Show All'}">
            <apex:commandLink action="{!setStep}" value="View" styleClass="btn" style="text-decoration:none" rerender="table,mine">
                <apex:param name="proId" value="{!pro.id}" />                          
            </apex:commandLink>
        </apex:column>
        
        <apex:column headerValue="Owner" value="{!pro.Process_Owner__c}" rendered="{!Filter == 'Show Others' || Filter == 'Show Other Completed'}"/>
        <apex:column headerValue="Contact" value="{!pro.Contact__c}"/>
        <apex:column headerValue="Reason for no Insurance" value="{!pro.Contact__r.Reason_for_no_Insurance__c}" 
                                            rendered="{!Filter == 'Show All' || Filter == 'Show Mine' || Filter == 'Show Others'}"/>
        <apex:column headerValue="Street Address" value="{!pro.Contact__r.MailingStreet}" 
                                            rendered="{!Filter == 'Show All' || Filter == 'Show Mine' || Filter == 'Show Others'}"/>
        <apex:column headerValue="City" value="{!pro.Contact__r.MailingCity}"/>
        <apex:column headerValue="Phone" value="{!pro.Contact__r.Phone}"/>
        <apex:column headerValue="Started On" value="{!pro.Start_Date__c}" 
                                            rendered="{!Filter == 'Show My Completed' || Filter == 'Show Other Completed'}"/>
        <apex:column headerValue="Completed On" value="{!pro.Completion_Date__c}" 
                                            rendered="{!Filter == 'Show My Completed' || Filter == 'Show Other Completed'}"/>
        <apex:column headerValue="Total Time (Days)" value="{!pro.Total_Process_Time__c}" 
                                            rendered="{!Filter == 'Show My Completed' || Filter == 'Show Other Completed'}"/>
        <apex:column headerValue="Outcome" value="{!pro.Outcome__c}" rendered="{!Filter == 'Show My Completed' || Filter == 'Show Other Completed'}"/>  
    	<apex:facet name="footer">Showing Page # {!pageNumber} of {!totalPages}</apex:facet>
    
    </apex:pageBlockTable>
    </apex:pageBlockSection>
    </apex:outputpanel>
     
    
    
    </apex:pageblock>   
    </apex:outputpanel>
    
    <apex:outputPanel id="mine">    
    <apex:pageBlock title="Complete Insurance Profile for {!con.Name}" rendered="{!showStep == true}" mode="inlineEdit">
    <apex:pageBlockSection title="Process Details">
        <apex:outputField value="{!selectedProcess.Start_Date__c}"/>
        <apex:outputField value="{!selectedProcess.Total_Process_Time__c}"/>
        <apex:outputField value="{!selectedProcess.Outcome__c}"/>
    </apex:pageBlockSection>
        
    <apex:pageBlockButtons location="top">
        <apex:commandButton action="{!saveProcessChanges}" value="Save Changes" rerender="mine"/>
    </apex:pageBlockButtons>
    
    <apex:pageBlockTable value="{!MyStep}" var="step" style="width:100%; border:1px solid #D4DADC;" rendered="{!showStep == true}">
        <apex:column headerValue="Name" value="{!step.Name}"/>
        <apex:column headerValue="Assigned To" value="{!step.Assigned_To__c}"/>
        <apex:column headerValue="Status" value="{!step.Status__c}"/>       
        <apex:column headerValue="Complete" >
            <apex:outputtext value="{!step.Complete_Step_From_Process__c}" escape="false"/>
        </apex:column>
        <apex:column headerValue="Log Activity" >
            <apex:outputtext value="{!step.Log_Activity_From_Process__c}" escape="false"/>
        </apex:column>
        <apex:column headerValue="Create Task" >
            <apex:outputtext value="{!step.Create_Task_From_Process__c}" escape="false"/>
        </apex:column>  
        <apex:column headerValue="Completed By" value="{!step.Completed_by__c}"/>
        <apex:column headerValue="Date Completed" value="{!step.Date_Completed__c}"/>
                
    </apex:pageBlockTable>
    </apex:pageBlock>
    
    <apex:pageBlock title="Activities" rendered="{!showStep == true}">
    <apex:pageBlockTable value="{!stepActivities}" var="act" style="width:100%; border:1px solid #D4DADC;" rendered="{!stepActivities.size != 0}">
        <apex:column headerValue="Date" value="{!act.ActivityDate}"/>
        <apex:column headerValue="Owner" value="{!act.OwnerId}"/>
        <apex:column headerValue="Type" value="{!act.Subject}"/>
        <apex:column headerValue="Subject" value="{!act.Navigator_Subject__c}"/>
        <apex:column headerValue="Description" value="{!act.Description}"/> 
    </apex:pageBlockTable>
    <apex:outputText value="No Activities Recorded Yet" style="font-weight:bold;font-size:large;" rendered="{!stepActivities.size==0}"/>
    </apex:pageblock>
    </apex:outputPanel>
    
    </apex:outputpanel>
    </apex:form>

</apex:page>

Controller

public with sharing class InsuranceCampaignMasterController {
    
    public List<Process__c> results {get;set;}
    Transient List<Task> acts;
    public Process__c selectedProcess {get;set;}
    public String Filter {get;set;}
    public boolean showStep {get;set;}
    public Process_Step__c step;
    public Contact con {get;set;}
    public String listTitle {get;set;}
    private Id processTemplate;
    private Id cID;
    private Id userID; 
    
    private integer counter = 0;  //keeps track of the offset
    private integer listSize = 10; //sets the page size or number of rows
    public integer totalSize; //used to show user the total size of the list 

    public InsuranceCampaignMasterController() {
        
        Filter = 'Show All';
        ListTitle = 'Total Not Yet Claimed : ';      
        ShowStep = false;
        processTemplate = [Select Id From Process_Template__c Where Name = 'Insurance Profile Campaign'].id;
        cID = [Select Id, Name From User Where Name = 'Chris Duncombe'].id;
        userID = userinfo.getUserId();
        totalSize = [select count() from Process__c Where Process_Template__c =: processTemplate]; //set the total size in the constructor
    }

    
    public Process__c[] getResults2() {
    	String soql = 'Select Id, Name, Process_Owner__r.Name, Contact__c, Contact__r.MailingStreet, Contact__r.MailingCity, Contact__r.Phone, '
                    + 'Process_Template__r.Name, Progress__c, Contact__r.Reason_for_no_Insurance__c, Start_Date__c, Completion_Date__c, ' 
                    + 'Total_Process_Time__c, Outcome__c From Process__c Where Process_Template__c = \'' + processTemplate + '\'';
        
                            
        if(Filter == 'Show All'){
          soql = soql +  ' and Process_Owner__c = \'' + cID + '\' and Status__c != \'Completed\' Order By Contact__r.LastName, '
          																						+ 'Contact__r.FirstName';
          totalSize = [Select count() From Process__c Where Process_Template__c =: processTemplate 
          												And Process_Owner__c =: cID And Status__c != 'Completed'];
        }
        if(Filter == 'Show Mine'){
          soql = soql +  ' and Process_Owner__c = \'' + userID + '\' and Status__c != \'Completed\' Order By Contact__r.LastName, '
          																						+ 'Contact__r.FirstName';
          totalSize = [Select count() From Process__c Where Process_Template__c =: processTemplate 
          												And Process_Owner__c =: userID And Status__c != 'Completed'];
        }
        if(Filter == 'Show Others') {
          soql = soql +  ' and Process_Owner__c != \'' +  userID + '\' and Process_Owner__c != \'' + cID
                            + '\' and Status__c != \'Completed\' Order By Process_Owner__r.Name, Contact__r.LastName, Contact__r.FirstName';
          totalSize = [Select count() From Process__c Where Process_Template__c =: processTemplate 
          									And Process_Owner__c !=: userID And Process_Owner__c !=: cID And Status__c != 'Completed'];
        }               
        if(Filter == 'Show My Completed'){
          soql = soql +  ' and Process_Owner__c = \'' + userID + '\' and Status__c = \'Completed\' Order By Contact__r.LastName, '
          																						+ 'Contact__r.FirstName';
          totalSize = [Select count() From Process__c Where Process_Template__c =: processTemplate 
          									And Process_Owner__c =: userID And Status__c = 'Completed'];
        }
        if(Filter == 'Show Other Completed') {
          soql = soql +  ' and Process_Owner__c != \'' + userID + '\' and Process_Owner__c != \'' + cID
                            + '\' and Status__c = \'Completed\' Order By Process_Owner__r.Name, Contact__r.LastName, Contact__r.FirstName';
          totalSize = [Select count() From Process__c Where Process_Template__c =: processTemplate 
          									And Process_Owner__c !=: userID And Process_Owner__c !=: cID And Status__c = 'Completed'];
        }     
            
        soql = soql + ' limit ' + ListSize + ' offset ' + counter;
        //System.debug(soql);        
        return database.query(soql);
    }
    
    public void takeOwnership() {
        
        selectedProcess = [Select Id, Name, Process_Owner__c, Start_Date__c, Completion_Date__c, Total_Process_Time__c, Outcome__c 
                                    From Process__c Where Id =: system.currentPageReference().getParameters().get('proId')];
                                    
        step = [Select Id, Name, Assigned_To__c From Process_Step__c Where Process__c =: selectedProcess.id];
        
        selectedProcess.Process_Owner__c = userinfo.getUserId();
        selectedProcess.Start_Date__c = system.today();
        step.Assigned_To__c = userinfo.getUserId();
        step.Status__c = 'Open';
        update selectedProcess;
        update step;
    }
    
    public void setStep() {
        
        showStep = true;
        selectedProcess = [Select Id, Name, Contact__c, Process_Owner__c, Start_Date__c, Completion_Date__c, Total_Process_Time__c, Outcome__c
                                    From Process__c Where Id =: system.currentPageReference().getParameters().get('proId')];
                                        
        step = [Select Id, Name, Process__c, Complete_Step_From_Process__c, Log_Activity_From_Process__c, Create_Task_From_Process__c, Status__c,
                                Completed_By__c, Date_Completed__c, Assigned_To__c From Process_Step__c Where Process__c =: selectedProcess.id];
        con = [Select Id, Name From Contact Where id =: SelectedProcess.Contact__c];
        acts = [Select Id, Subject, Navigator_Subject__c, ActivityDate, Description, WhoId, OwnerId, WhatId From Task Where WhatId =: step.id];  
  
    }  
    
    public process_Step__c getMyStep() {
        return step;
    }
    
    public List<Task> getStepActivities() {        
        return acts;
    }
    
    public void saveProcessChanges() {
        update selectedProcess;
    }
    
    public PageReference Beginning() { //user clicked beginning
      counter = 0;
      return null;
   }

   public PageReference Previous() { //user clicked previous button
      counter -= listSize;
      return null;
   }

   public PageReference Next() { //user clicked next button
      counter += listSize;
      return null;
   }

   public PageReference End() { //user clicked end
      counter = totalSize - math.mod(totalSize, listSize);
      return null;
   }

   public Boolean getDisablePrevious() { 
      //this will disable the previous and beginning buttons
      if (counter>0) return false; else return true;
   }

   public Boolean getDisableNext() { //this will disable the next and end buttons
      if (counter + listSize < totalSize) return false; else return true;
   }

   public Integer getTotalSize() {
      return totalSize;
   }

   public Integer getPageNumber() {
      return counter/listSize + 1;
   }

   public Integer getTotalPages() {
      if(totalSize == 0) {
      	return 1;
      }
      if (math.mod(totalSize, listSize) > 0) {
         return totalSize/listSize + 1;
      } else {
         return (totalSize/listSize);
      }
   }
    
    public void viewMine() {
        Filter = 'Show Mine';
        showStep = false;
        counter = 0;
        listTitle = 'Total Open By Me : ';        
    }
    public void viewAll() {
        Filter = 'Show All';
        showStep = false;
        counter = 0;
        listTitle = 'Total Not Yet Claimed : ';        
    }
    public void viewOthers() {
        Filter = 'Show Others';
        showStep = false;
        counter = 0;
        listTitle = 'Total Open By Others : ';        
    }   
    public void viewMyCompleted() {
        Filter = 'Show My Completed';
        showStep = false;
        counter = 0;
        listTitle = 'Total Completed By Me : ';        
    }
    public void viewOtherCompleted() {
        Filter = 'Show Other Completed';
        showStep = false;
        counter = 0;
        listTitle = 'Total Completed By Others : ';        
    }
}

Thanks for the responses ~ sfdcfox ~, you definitely got me going in the right direction with the dynamic table and the dynamic SOQL.  

Chris