RE: Pinch Seams.... Look just in front of your rear tire, where the metal from the tub appears to be pinched/welded together, there is a 90* angle. THAT is the pinch seam that everyone refers to. A lot of times, it needs to be cut back to make clearance for larger tires.
I had to trim mine back about 3" to fit my 37's. Use a Sawzall to cut it. Then touch it up with some spray paint so the cut edges do not rust. If you have Rubi rock rails, you may need to trim those too (I had to do this too). Just remove them (3 or 4 bolts), pop off the end cap, cut the rail, put end cap back on, bolt back on.
RE: Bump Stops... Go to a sports store and buy some practice hockey pucks (1" thickness; ~$1 each) and go to a hardware store, buy a bolt that is about an inch longer than the amount of bumpstops you wish to run, and a washer and bolt. Remove the front springs, drill a hole through the bumpstop pad wide enough for your bolt, drill same size hole through the middle of your pucks, stack them, run the bolt through the pucks and the hole, bolt in place. Much cheaper than spending $30-70 for manufactured bumpstops. Using this method, I have adjusted my bumpstops w/o having to remove the front springs, once I had the initial hole drilled. Hope this helps you save some money!
For reference, I have a 2.5" lift, and 37's. I run 3.5" bumpstops in the rear, and 2" bumpstops up front, with trimmed flat fenders.
2008 JK Rubi on big tires and stuff, RIPP supercharger.
Various dents and scratches.