When you say the mirror doesn't quite work, does that mean you can't really see out of it?
I'd start filling the gaps between the fenders and bumper as well as making an air dam down from the bumper to guide the air around the sides instead of underneath. If you haven't installed smooth wheel covers (coroplast or pizza pans etc) they would also be a good idea.
Honestly all Wranglers are aero messes so you'll basically need to fabricate some body surfaces to make it work well. (such as the gap fillers and air dam) This doesn't mean it's not a good idea; it will just take more work to get it to perform!
Actually, if you're down for it, building a boat tail shouldn't be too hard, given all the mounting points built into a Jeep. Could you find an extra hardtop to cut the back out of in order to anchor a boat tail? You could see a good 20% highway fuel economy increase from a boat tail.