Windshield Frame and Dashpad Replacement
Pfreen.... In seeing your post, I decided to finally post up some BTDT of my experience. I've an MKIA w/ 5 studs for frame, did not use the alignment studs and was able to get good alignment with the quarter window. It is a little bit premature to say I have 'perfect' alignment with the hardtop, but I have clamped a dry fit down. You may be interested in some of the insight. YMMV (Your mileage may vary) of course...
Some of the dash pad tips may help with windscreen / windshield frame alignment and you may wish / choose to look at these areas prior to reinstall.
I just uploaded a number of tear down and refit picture of this area. In my opinion, the key points may be: dashed foam thinning, correct rubber seal fitting under frame, with seelastik (tape caulk) replacement and added corner post rubber wedges (pic added). There were also multiple washers placed on the studs under the scuttle, prior to multiple nuts. Likely also there to align the frame and allow sufficient torque.
As many of our prior posts with pictures were lost, I'm afraid that for this number of pics I'll ask that you visit the website...
http://www.lifeofti.com/windscreen.html