It sounds like you should be in pretty good shape as long as it passes emissions for a CJ-7 (shouldn't be tough with that new of an engine). As I'm sure you aware, most shops realize they could lose their license if they pass any vehicles that shouldn't pass. I think if the tires are barely hanging out of the fender flares, you should be OK, but strict (and correct) is that the fender flares must cover the tires and you need mudflaps on the rear.
You just need to go to your favorite shop and have them do kind of a quick, visual inspection and see what they 'flag'. Address those issues and take it in for it's emissions/inspection and see where things go from there.
With my YJ, I'm making sure I have the flares covering the tires, mudflaps{removable is fine}, a newer engine than the VIN/Title complete with all the emissions gear for the engine of origin(vapor cannisters, cat, etc.), and it meets the lift laws.