Before you go any farther, if you haven't done it already do some measuring and leveling to check the flatness of the rear torsion tube.
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A Bug pan can get twisted. Since my black buggy's pan was base off a Baja that was horribly built, plus the driver's side floor pan was rotted out so bad I had to take it down to this. I replaced both floors but the material they were formed from was just too thin for what I thought I would need so I bought another pair of thicker material pans and installed them.
The rear torsion tube can get twisted in relationship to the tunnel so double check it before you get too far into things. With the rotisserie I was able to turn the tunnel part upside down and check the wings on the tunnel to find out if the tunnel was still square front to back then... I started from there.
I got this from talking to several bug guys plus a couple of dune buggy guys plus one owner of a VW bug wrecking yard. Opinions are often starting places and if the opinions match... they might be wrong too!

Usually you can get some good out of them so it is worth the time and conversation.
One thing I did find out from the wrecking yard guy was that with a glass body on the pan the tunnel behind the Napoleon's hat and the shifter hole can get a slight "swayed" shape to it so the tunnel "racking" (a slight twist in this case) is something to check.
On the front cross piece over the Napoleon's hat area on my blue buggy I did use one of the light weight commercial body lift pieces (the rest of the lift was so rotted it wasn't usable even as a guide). I did stiffen up the bottom of the ends as body mount bolts went through the slotted holes so I wanted to be sure things were OK.
On the black buggy the changing of the pedal assy required something different done.
As far as the trans and that stuff I can't help much there. I use 6-rib bus boxes or the stock IRS boxes in my buggies.
Lee
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