Alright. TJ flares part 2 happened today. Scan back through the thread for before pics of the rear flares. Here's a quick step by step.
1 - remove old flares and fender liners (optional, but the liner becomes a PITA if you try to keep it)
2 - apply a bunch of masking tape around the wheel opening. This helps save your paint while you cut, and gives something to draw the cut line on
3 - clamp the TJ flares in place and trace your cut line. I lined up the front of the new flare with the stock wheel opening
4 - Cut out the traced line. IMO this is best done with a jigsaw and from back to front. You have more control than a grinder. I've done it both ways, and the jigsaw is definitely preferred. After the initial cut (purposely a little smaller than final), I used a grinder w/ a flap disk to smooth all the rough edges and slowly open up the cut to the proper fit.
5 - After you have the flare fitting properly, clamp it back in place and mark holes to be drilled. I chose to use the original 3 holes in the front on each side and drilled holes in the flare to match. The rest I marked on my tape which was still applied and drilled the new holes to match the existing holes in the flares. Install the flare using the original hardware
6 - pile all the tools you ended up using during the install onto your service cart so you can get it all back into the garage
7 - admire your work.. Still need to plasti-dip these flares but I didn't have time today
8 - Optional. I wanted to keep some of the protection of the fender liner where is shields the drain channel under the floor, and in the back to protect the light wiring. I had to cut the liner up a bit to remove it so I just used 2 sections to cover the very front and very back of the inner fender. I'll be spraying bed liner inside the fender as well once we get a chance to pressure wash some mud out.