I'm only suggesting things, I am not saying that you didn't already check, etc.
Based on my logic, there's no reason for the intake air to heat up unless it's being compressed!
If that's true, why isn't said boost reaching your intake?
Also, how to do you explain the boost falling off a cliff once the vanes open?
Regarding the charge cooler. I'm not suggesting that it's not better than what you replaced, but I am saying that I would want it to cool more. A good design FMIC (air2air) system usually cools within 6-12dec C of ambient (on a properly setup FI system, etc). On a similar vehicle, a good design water2air system should be able to come within 8-12deg C of the afore mentioned FMIC setup. This is all on a vehicles that's moving, aka street\track car, not drag or offroad setups. This is why I'm not happy with your current charge cooler, although I do understand its benefits and appeal as far as reducing charge piping and improving response, consistency, etc.
Regardless, I'm not trying to hate on your setup, I'm only trying to suggest stuff that might help you sort things out or trigger input from others that may help.
The way I'm reading your graphs, once the vanes open up, your EGTs go haywire which I can only explain by the fact that your boost falls off a cliff and you're still dumping fuel (are per your maxxed out injectors at 2800rpm comments) but don't have sufficient air to burn it.
I really think you should log AFR to see if it reveals any clues.