It appears the Contact Role is an embedded related list in the code and therefore I can't trigger a field update on conversion to set this checkbox. I was able to find the file using sforce explorer but don't know the best option to implement around it. Contact Role Primary = "o.IsPrimary"

It would appear that all converted LEADs into an Opp would have this defaulted to Primary since that is where the primary opp came from. 

Thanks,