I have a 1996 Xj in decent shape but the a/c quit last year and i am not going to fix it because the vehicle is only used in the winter.... I have to replace the transmission cooler so I was wondering while its out should i remove the A/c condenser to increase air flow to let the vehicle run cooler? or would this cause a problem because the secondary fan runs off of the a/c system

There is no chance I will ever want to repair the a/c and when I am done with the jeep it will be taken away in a dust pan so i am not worried about selling it to anyone that might want to fix the a/c

Yes you can.

The temp sensor for the electric fan is in the radiator.

Oooohhh.... On-Board Air Compressor Conversion!!!