The pictures help a lot. And they created another "Deja Vu" moment. It took a while to find since we all tend to call parts by different names, but here's a recent thread on the same part:
https://cj3apage.com/Forum/index.php?topic=5392.msg40906#msg40906I will guess that the parts factory that most vendors use have determined that the plate under the bracket isn't needed. I can't explain that mindset.
I don't know what the best solution is for the battery box lid, but I can actually see myself cutting a notch in the seal way before I start redrilling pivot bracket holes - as that could lead to other fitment problems (you've mentioned a couple so far). You can't be the first to have this issue so surely, someone else would have an example that shows the solution.
Oldtime's description of the narrow cowl may explain my issue with an aftermarket windshield. Initially, my original w/s had a lot of PO damage (a wildman with a power tool is a dangerous thing). I was offered an aftermarket w/s and took it. To make it fit on my original cowl. I had to bend the arms OUT to get them to straddle the cowl and connect with the brackets. It's now bent correctly to fit. In the mean time, I found a body shop that had the ability to fix my original; problem solved.
Initially, I thought your arms might have been bent in a way to allow more backwards lean, e.g. like too many people pulling on the w/s frame to get into and out of the jeep. Bending the arms sideways to fit the cowl was relatively easy - just a little at a time and it would align better with the cowl. However, since your actual issue is the opposite, a thicker spacer would make much more sense.
I'm not seeing all the misalignments you're having to work with but it's possible that pushinig the pivot backwards has tipped the w/s frame forward up at the top. Since you're comfortable with fabricating, try duplicating the original size/placement of the added plates and position the w/s without the seal to see if you can get it to sit on the edge of the upper cowl as it should and then use a spacer to duplicate the height of the seal to see if you're still having clearance issues. The diagonal slot in the bracket should allow enough available adjustment to give you the needed 66.5" for your TigerTop.
Added: Looking closely at your instrument panel "overhang" I don't see much there. Maybe it's more pronounced in person. Also, studying the pivot images closer, you've got both brackets adjusted full down. In my mind, that positions the w/s in a more upright position - lengthening the distance you're measuring for the TigerTop. Try repositioning the brackets where they are slid fully the opposite way - then remeasure and test battery lid clearance.
