This all started happening after turning on an amp that I probably installed very poorly

One day the Jeep didn't start. Lights came on but nothing when I tried to start. No clicks. Unplugged the fuse to the amp and it started right up. Took it to oreilys to get the battery tested. Reads bad battery. We put a new battery in and it still stuttered to start. Test the new batter, says it's a bad battery. Try again, it says that it's wired backwards. It wasn't. Put the old battery back in, test came back fine, started up alright but not great. I replaced the corroded positive line going to the battery and it started up just fine for a few days.
Today it started to really struggle to start and I can feel the problem coming back. Not sure what's causing the issue.

All fuses are good. Alternator, starter, and battery tested good

Thanks in advanced

 

Look for a corroded negative line. Start there. Both of them.

 

The bit of cable going to the battery on the negative side was replaced last year. Still looks fine

 

If this just started after installing an amp, then you know it's related to the amp.
Double check all the amp wiring and make sure your grounds are clean and tight and the battery cables are clean and tight.

Is it possible the amp is drawing a ton of power such that the starter can't get enough juice or the alternator can't keep up with demand?

 

I mentioned in the original post that the issue came back after removing the inline fuse from the amp, essentially taking it out of the equation

 

Sorry, it wasn't clear what the current state of things are.

Amp related doesn't necessarily mean the amp itself. You were undoing battery cables and had your hands in the engine compartment - you could easily have jostled a ground wire during that process. You could have not tightened the battery cables down tight enough - they need to be clean and super tight. You could have blown out the battery, alternator or voltage regulator if the amp is poorly wired or requires a huge amount of power to operate.
An XJ needs the battery to be in good shape - they get very grumpy with "less than proper" battery function.

The mention of " This all started happening after turning on an amp that I probably installed very poorly " is a huge clue to where to focus on for what the root cause of your problem is.