Newbe builder starting a grand project

[jonnyNITRO]

Well, the Thanksgiving holiday set me back with a ton of work to catch-up with. I'm back at it.
So, I noticed that the Toyota back window bulges out along the lower half of the cab. This is what must used to make room for the mechanism. The tailgate windows have the same (extra) space behind them making the thickness of the tailgates bulge out or taper in for the glass to lift straight from the groove.

I suppose I could modify the back of the cab slightly for the necessary angle. Not sure I want to hack up my roof though.
This is a tough call since I really like the idea. Just don't know if it's practical for this truck body.

Question:
Do the side markers fit the same front to back? In other words, can I take a front, side marker and use it in the rear instead?

Question:
What's the best way to remove rust from the metal panels that make up the roof? I know I must have rust in there. Is there a gel or spray that dissolves the rust? Really.