transmission problem

hey guys,
i had the tranny in my 98 GT (3.8 , 190,000km) rebuilt last october. Last month, it started shifting really rough after the car had been driven for a while (it drove perfect when the car was cool). I brought it back to the mechanic and he said it was getting overheated, so he installed a transmission cooling system and did a transmission flush (for an additional 400 bucks). Since then, the performance just hasn't been the same. The accelleration is not what it used to be, and even though it doesn't shake hard like before, the gears don't shift smoothly. By looking at the RPM while i drive it's like the gears switch too fast or too slow and sometimes it seems like it gets stuck in second for a while. By reading this forum i gathered the tranny flush might be responsible for the problem. My question for you fine gentlemen is: is there anything i can do? Can i bring it back to the guy or is this something he wont' be able to fix? My warranty expires next october so if the problem can be fixed i'd like to be able to do it before then.
Thanks alot for your help

Find out what he replaced when he "rebuilt" your trans. If he didn't change the PCS and all the shift solenoids , that's where your issue is.

thanks for the reply.
The funny thing is the car drove awesome after he worked on it the first time, except for when i drove it for a while and it started shifting rough once it got overheated. That's why i'm thinking maybe it was the flush. When i got it back the second time is when it started shifting weird even when the car is cool.
Thanks for your feedback