The previous owner of my XJ deleted the entire AC system. I lived with it last year, not doing it again. My question is why delete the AC and with so many aftermarket options out there for a compressor which ones are good. Thanks for any and all help.
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Why delete? He had trouble with it. Stock OEM XJ compressors are generally good.

 

It's possible the evap coil is leaking and he decided to just delete the a/c instead of removing the dash. It's also possible the compressor was bad or o rings were leaking. Who knows?

Either way, I'd go to a junkyard and pull one out of a Jeep. The ones online tend to be a crapshoot sometimes. You might as well take this opportunity to replace the o rings in the system. You can buy kits on jeepair.com.

 

I've heard that it'll give you an extra 10 horsepower. I'm not sure about y'all but the cherokee ain't no dragster! I'm going to be nice and cool in the woods. Or on the street.

 

Yeah, I wouldn't spend a lot of time worrying too much about how the P.O. was thinking. Any number of reasons are logical - from horsepower to cost.

It is definitely good advice to check that the evaporator is functional - if the P.O. let the compressor fail and it shot metal shards through the system, you don't want to blow a new compressor by hooking it up to a contaminated system. Also, if it's leaky, you want to know that up front.

I'm not familiar with the 99 system, but I did the A/C in my 95 with excellent help from this forum and it blows nice and cold. I ended up replacing everything but the evaporator and was fortunate that it was solid and has held up going into 2 full years.

The compressor is obviously the biggest cost for the component. I used an aftermarket compressor (replacing the old one that was sounding sketchy and hopefully preempting the compressor failure, metal fragments issue) and it's working. It's louder than I'd like, but sounds a heck of a lot healthier than the one I replaced.
The evaporator is the hardest part to replace since you're going to be pulling the dash like a heater core. When I did my system, I took the chance since the compressor ran and the other parts were roughly $100 and I figured worst case I'd learn a lot and get some hands on experience. I only sunk the couple hundred on a new compressor after knowing that the rest of the system was working.

So in your case, with the A/C was deleted, I'd definitely want to be pretty damn sure the evaporator was OK. If you can find a junkyard compressor for a good price, I'd probably at least -start- there and make sure the system will work correctly if you go the route I did. The other option is to have a professional A/C shop take a look and see if they can confirm that the evaporator is OK and not contaminated with metal fragments.
I doubt the O.P. deleted the A/C if it was working perfectly.... best case an o-ring failed and the refrigerant leaked out and they just figured they'd get rid of it. I would strongly suspect though that they had either an issue with the clutch which meant either a (reportedly difficult) clutch replacement and/or a full blown seizure and knew the system was hosed and even a new compressor was not going to correct the system (metal particle contamination).
Again, who the heck knows with people... I'm constantly amazed.... but I personally would only "delete" an A/C compressor if I HAD to - meaning the normal "disengaged" pulley function was not available. I had the A/C fail in my last Jeep and drove it for like 9 years without working A/C and never removed the compressor.