I'll chime in, these might be terribly obvious but I have to ask anyway.

Did you bleed air out of the coolant system after all this work?
Any water in the oil (Milkshake)?
Does your radiator cap have crud all over?
Last time your coolant was flushed?
Still running dexcool or have you swapped to conventional?
What mix of coolant to water?
Ever have the intake gaskets replaced?
Any seepage from the intake gaskets?
Have you had the cooling system pressure checked to make sure there are no visible or noticeable leaks?

I dont check the 3.1 section as much as I used too, I had a 96 gp with the 3100 then swapped to a 03 3400, these were things I had to check when I had a issue with mine, turns out it was the plastic felpro intake gaskets I put on when I had my new motor on the stand. Well that and the temp sensor for my gauge cluster....

anyways reply with answers and I'll try to help you. Good luck.