I quickly went through the entire post and I think I have the gist of the problem and what you've tried/replaced to resolve the problem. The main problem I see is air flow on the radiator. As Fordum mentioned, you should try moving both the oil and trans coolers out of the way temporarily. Could probably do that with just a couple lengths of hose and couplers along with some simple brackets. It's cheap and shouldn't take that long to try this test.
I'd also remove the fan shroud and fan so you could measure the temps with your IR gun at different spots on the radiator while in your driveway. Maybe even take it for a drive before doing this so the tranny heats up. And as mentioned in this link, you can measure the temp of your cat to see if it's blocked. It says a difference of 200* between the inlet and outlet means that it's blocked (or a pressure reading at the O2 sensor of 4 or 5 psi).
http://www.buzzle.com/articles/clogged-catalytic-converter-symptoms.html
As a final thought, it seems like you've dumped a lot of $$ into replacing parts but you don't want spend the money on a fan cooled trans cooler. I think they're a wise investment to make sure the trans stays cool. Not only does it move it away from in front of the radiator where it's restricting air movement and blowing very hot air onto it, but I think they're more efficient.