I will leave this here to help someone out in the future who's having the same questions as me.
A 2006 engine will work in a 2002.
Moreover this means that all 2000+ TJ engines, to my knowledge are able to be swapped with one another.
The biggest change was using my 2002 OPDA/CPA in the 2006 block.
I am running mostly 2006 accessories (alt, water pump, compressor, tensioner) but using my 2002's power steering pump.
Now the interesting part, and different issue altogether is that my 2002's OPDA/CPA had the same wearing patterns as the notorious 05/06 models. I'll put some pictures of the worm gear up later.
Edit: and here are the pictures of the worn OPDA
If anyone has questions about swapping in a newer engine in the future, PM me and I'll see if I can be any help