25 tow vs. 40 tow tunes
 

What is the difference between these tunes, besides the obvious 15hp? Is the trans shifting the same? Would the egt's be lower?

Actually, there are a few substantial differences between those two calibrations.
Most notably, the 1-2 shift speed, 2nd gear TCC apply, and fuel rate/ICP.

The 25T will run similar to a stock truck with a slight increase in power and efficiency and will be slightly quieter than the 40T.

So will that effect egts, or just the trans?

Well, since there is less fuel, the EGT will be lower.

I can't see how you are actually having an EGT problem with stock injectors though.

I personally have two customers that have nothing more than an aftermarket exhaust on their trucks and tow insane amounts of weight in 60+ HP tunes with their 97's.

I know you have an EGT thread.....but I think you have something going on. 10-12 PSI on a stock OBS turbo is about maximum regardless of tuning so I wouldn't call that a problem.