Sorry, got to disagree. They are VERY different. I have the original AC system out of my late model CJ-7 and swapped in a complete 1991 YJ system. The OEM CJ unit is going into my 83 Scrambler.
Like most auto parts, they love to change the parts over the production run of the model just enough to make them look the same, but they don't interchange. The CJ AC unit is made by American Air and I believe the YJ units are too or from a new version of the same company....too many little signs that they are the same. I compared 3 YJ and one CJ system to gather this info.
The CJ system uses the cone or flair connections through the whole system...like a brake line. The YJ uses O rings. The compressors are different and have different pullies unless you have the serp belt CJ (CA models).
The later YJ underdash unit (91 on) has clips that hold it together and can easly be taken apart and cleaned out. The evap has 90 degree bends that only work with the YJ main lines. The CJ and early YJ units are glued together and don't come apart. Yes the front 3 vents are different too. CJ straight, YJ 45 degree upward. That part can swap between the two. The CJ condenser is a twin tube style and has large side brackets with the dryer attached to the passenger side. The YJ is a serpentine style with a seperate dryer attaching to the passenger inner fender. There is more, but that the main differences.
I swapped in a 94 stroker 4.6 and wanted to have AC. While i could have used adaptors on the compressor, I went with the more efficient YJ system due to the improved condensor. The dash unit matched the compressor and the upward vents are a plus, but I'm torn as they don't look like the ol CJ type. After i searched for months to find a bad CJ condenser to cut the side brackets off of, I modified the YJ condenser with my own brackets to copy the CJ style. There is a universal style at Jeepair.com. I'm still working on it, but have many good pictures if you need them.