Good idea to get rid of the modified air cleaner, those things are not worth it. I would be tempted to put a mild lift (2.5in) and some 32/33 inch tires on it. But I agree, the stock look, especially (for me) the fenders and flares look the best. Though those longer wheel base jeeps look great with a bit of beef, in my opinion.
I am currently rebuilding a 1997 TJ, SWB. I welded the floors behind the driver seat with replacement panels and now I am looking at painting it; bought all the paint sprayer stuff this past week... lots to learn. All stock, no lift, no big tires yet. That will be next. They are a lot of fun.