Hesitation/Slipping Sensation...Help?!?

Hey guys I need some help. I have a 96Gt with an automatic transmisson. No mods and no rebuilds or anything. I just had the motor rebuilt and havent yet put no more than 5k miles on it. However the tranny has 158xxx miles on it. The problem I am having is that when I am driving and I am just doing city speeds of say between 30 to 45 mph the car starts this hesitation/slipping deal. It only does it when it is under 2k rpms though. If I am over 2k rpms it doesnt do it which leads me to believe that it isnt the tranny going bad. However before the motor rebuild the car was drove around with 3 misfiring cylinders and some other issues (not by me but by previous owner). So could this mean the cats are starting to clog up? Or could it be the transmisson modulator switch? Or is there any other sensor or anything that could cause this? The fuel filter was also replaced less than 10k miles ago, prolly hasnt even got 5k miles on it, so I dont think it could be that but since its cheap I may replace anyway. I just replaced the plug wires since the shop that rebuilt the motor threw on mismatched wires ( 8mm & 8.5mm) and to top it off they also put on 2 wires that were damned near long enough to reach the firewall and back to the coil pack. I am not sure however if they replaced the plugs so that is another thing I am going to replace but I wouldnt think plugs would be the cause of the problem. If anyone could help me figure out where to look for possible solutions would be greatly appreciated. I dont have the $$$ to go to a shop right now & then hear them say "Oh well you need this & this & that" esspeacially since I can do most the work myself. Thank you all for any help.

The trans fluid level looks good on the dip stick and obviously had just been service just before I got the car because the color is still a nice pinkish/reddish color and doesn't feel grimy nor any metal shavings present. So I don't know if I should consider the fluid conversion or not. But I will keep it in mind. Thanks Burns anything else you would consider looking at however?