Hey, I just finished installing my Bestop Tire Carrier too. Tomorrow I'll mount the tire...wanted to take some pics first.
I had a problem with the jack nut, too. I found the thread size correct, but the supplied 1/4-20 bolts to be too short to thread into the jack nut to compress it. Fortunately I scrounged around an found a 1/4-20 bolt about 1-1/2" long an it worked perfectly to compress the jack nut. Then I was able to use the supplied 1/4-20 bolt to tighten into bracket.
I too drilled all the holes according to instructions...and then found the Upper Backing Plate didn't line up with the holes.
The Upper Backing Plate, for those who haven't installed this carrier, is the brace for the Upper Body Hinge and is mounted onto the roll cage. I figured I'd probably have to re-drill the holes, too. A body shop friend of mine looked at it and said he'd just tilt the backing plate down to toward the holes in the body, get the body hinge, gasket, and bolts started into the backing plate, tighten them up and then tighten the roll cage bolts down. I doubted...and I was wrong! After staring at the mis-aligned holes (my upper hinge holes in the body were maybe 3/16" too low) for a while, I decided, screw it, and just started putting the Upper Backing Plate, Upper Body Hinge, gasket, and bolts together and tightened everything down. Darned if it didn't work!!
My friend said the corners of the TJ are incredibly strong. I understand that now.
BTW, the supplied gasket for the Upper Body Hinge was the wrong size and the holes didn't line up. I cut the third-light gasket down to fit the hinge and punched two holes in it to match the hinge.
I wasn't planning on re-mounting the third brake light anyway.
Now I just need to work out the adjustment/alignment and fit of the door. Uf20wop, how did your tailgate align? Looks like mine is pushing out a bit at the top. I will have to work on that tomorrow.
On a side note...have I mentioned lately how much I hate torx bolts? I managed to strip the heads of both roll cage T-50 bolts. I have found the easiest way to remove bolts like this is with an air hammer and chisel. Actually my body shop friend did this for me. Had them loose in about 5-10 seconds. That is how we also removed a stubborn windshield hinge bolt. Craftsman has a nice air hammer for $34. Think that will be my next tool purchase!!