I got a new battery a few months ago and after about 3 weeks to a month of having it, my 98 Cherokee was having battery draining problems when it would sit and be turned off for more than an hour or two. Took it to auto store and everything tested fine, the battery just didn't have a full charge, so they charged it up and I put a quick disconnect negative battery cable on so I could unplug the battery overnight and prevent drain. It starts rough but it starts nonetheless. I went out today and plugged the cable in and it won't click or turn over. All the electronics turn on but it won't crank. What's the deal here?

Starter, any and all battery cables, grounds, wiring short to ground, alternator/voltage regulator, the newish battery...all are possibilities.

I think you need to take it in and have a full diagnostic done. It's going to be hard to fix this over the internet.

They should 'load test' that battery or replace it under warranty. Once a lead-acid battery is drained empty, it never fully recovers.
Also, by disconnecting the battery overnight, the computer could be resetting itself to factory parameters each time. Causing it to 'relearn'.

Was there a problem with battery draining (parasitic draw) before this battery was installed?