Huh. You're sure? I don't mean to doubt, but in photos I've seen listed a 3/16" difference in shaft length from the end of the splines to the carrier bearing. That seems like enough to cause problems.
I've also got a good friend who owns and autocrosses a GT and a GTS, and also is a professional mechanic. He is the one who told me that the AT shafts aren't interchangeable.
Honestly, if he lived within a few hours of me, I'd just drop the car off with him and pay him to take care of it for me.
Can I ask where you purchased your axles?