A Challenging Problem :S

I have an 1995 Eagle Vision ESi V6 3.3L (by Daimler Chrysler) with a longitudinal automatic transmition. At 400 000 Km, the STOCK transmition started having problems. As I quickly accelerated from 0 - 60 km/h there would be a loud CLICK and you could feel that the car has a shifting problem. However, the car has a safety mechanism that it doesn't shift above 2nd gear if it senses a problem in the transmition or the transaxel when this click occured. So the car was taken in to install an imported year 2000 transmition in it because it was noticed that my transmition's sprokets were worn out. The new transmition didn't fix this problem. So they replaced the sprokets in the car's old transmition and replaced the oil/filter. This worked for about 2-3 months but then the problem re-appeared. :confused: This rebuilt transmition has only spent 50 000 km so far and when I accelerate too fast, the click occurs again. So what do you think the problem is and what can I do to fix it?

THANK YOU VERY MUCH FOR ANY HELP.
IF YOU NEED FURTHER INFORMATION, PLEASE ASK.

Notice: The dealer is a rip off. They will charge me 75$ an hour (upto 5 hours) of inspection time only. Even if they don't find the problem, I'm still paying the full price. They suspected it was the ECU but they said that replacing it without inspectiong might damage the new ECU. They're a bunch of dumb shits following some fucked up protocal that has a very large stick shoved its ass.