Need help repairing my rear fender..

First thing is, I don't want to run flares. I've never had a problem with the law here, and I hate the look of flares on my XJ. I had Bushwackers for a week, and took them off. I've cut-n-folded my rears and the passenger side looks fine, but the driver side came out terrible, especially after the flare install. I'm just looking for some idea's on how I can repair this mess. Keep in mind, I don't really want to cover it up...

You can't replace the rear unless you cut it and weld in a new one. My recommendation would be to fill the holes (weld, bondo, jb weld) smooth it out, and paint from the body line down with either a flat black or bed liner. For the fender try and make a few more cuts and bend it so its rounder. I made lots of cuts and mine is pretty round, but if I wanted to talk the time I could have done better

So you're saying, make more cuts on mine after I already rolled it, and it should come out better? I'm not worried about the holes, I am just going to paint them and throw THOR guards over them.

Or maybe pull all the folds back down so I can straighten it all out, make my cuts, and re-fold?

take your time and try to shape the metal. more cuts will help with getting a better radius. a hammer and dolly afterwards will clean everything up and make it look real nice.

I realize I should have made more cuts to get a better radius, but now that it's already cut and folded, what can I do? Is there any hope in getting it to look nice, or should I just resort to flares?

Partially unfold them, cut them more, and re-hammer them over. Then give it plenty of love with a hammer. You can fix that.
As for the holes, personally I welded mine, but you can use bondo as mentioned above.