First off, did they ever come with a limited package.
mine was sport but I feel like I saw some with power options when I was searching on CL... I might be making that up though :dunno: Also by now you can find most of the 'limited' options in the JY and swap them in (including power seats from a 4 dr as long as you transfer your flip forward lever and other hardware from the 2 dr seat IIRC, I think I saw a writeup somewhere)
Second, did they ever come in a charcoal grey color?
No clue but you can buy the Jeep cheap enough and paint it at Maaco. Just do the prep work yourself and maybe spray under the hood and inside the door jams etc with a similar color to what you will be using before getting it sprayed by them (IIRC they don't spray under the hood or inside the doors if you get the cheap paint job).
Third, did they ever come with a grey interior?
yes, mine was/is grey
Fouth, what year did they change the rear side windows.
As was already mentioned I have seen them on quite a few years, I believe it was an option which (surprisingly) it seems not many people got, maybe it was a pricey option? I swapped the vent windows onto my '93 since I didn't have them from the factory