I am having issues with my AC relay fan on my jeep. The fan kept on running after I shut down the Jeep and hence drained the battery. Had to replace the alternator and told my mechanic to remove the ac fan fuse. What are the consequences in doing this. Tired of putting money into this thing.

The simple way would be to turn A/C off before turning engine off. See if that help. It my be in the switch.

On some WJ's the ignition switch going bad could cause your problem.
Read this, near the bottom of the page. http://www.wjjeeps.com/blower_motor.htm,
look under Blower Motor Diagnostics, #6. Ignition Switch.
And Welcome to CF!

I had the same problem...but thank god I found out about it after 45 minutes only.
But then when I started the car it never came on...even when the a/c is on.
I replaced the electrical fan relay an it solved the issue.

Was that the relay under the headlight that you replaced?

mine has been doing this off and on lately. what i have done is i just pop the hood, undo the quick connector for it and then plug it back in once i am ready to go again. I plan on splicing in and putting it on a 3 way toggle switch that way i can run it as a normal ac fan flip it to manual on and have it run a constant on the trail and have the ability to run a manual off just incase i wont turn off when i shut the car off

That is correct, the passenger side on my 2001 GC. It wasen't east to reach but with the help of a friend I did it. Hope this solve your problem.

The A/C relay was not working and so I had them pull the fuse. 400 bucks to take the bumper off, grill and the right head light. I've put so much money into this Jeep, swearing I'll never buy another one. Oh by the way! The part is only 80 bucks.

Man..I did it myself...I guess you could have done it yourself with the help of a friend maybe. By the way, the relay should cost around 5o $, you really paid too much for this.