Here is a thread that is in the HOW-TO section that shows Transgo shift kit instructions. You will follow everything to put it back together aside the Transgo springs and spacers which are not used from the factory. You will simply have two larger diameter springs on the bottom side of the accumulator pistons and they are both the same. Make sure you use the correct piston in the correct bore as the top side smaller spring is larger for the 2-3 side which is noted in this writeup. It sounds to me like you may have taking the tubes out of the accumulator assembly and put the two small tubes back in reverse order so definately compare the pics I have with what you have on your car. It is also important to properly torque all of the bolts or you can have cross leaks or warp the parts which also causes cross leaks. If you reused the original gasket plate that can also cause leaks and it is not something I suggest trying to reuse because any leaks in this area will cause low pressure which will cause slippage.
Here is the link with the writeup
http://www.grandprixforums.net/shift_kit.php