In regards to the quarter panels . . . First I need to mention that your NOS quarter panels are 87-93 style as an FYI. Not a deal breaker, but if you weren't already aware the quarter window area is very different from your original panels and will require additional modifications to allow the re-installment of the original quarter windows and trim. I would also mention that you might want to consider finding some of the later 4 Eyed quarter window trim that use the clips rather than the folded over metal to help hold them in place.
To do a full quarter replacement using the panels you have will require that you cut all the spot welds that hold the current panel in place and remove (obviously right!
). You will have to separate the overlapping metal by either moving the metal pieces completely to allow access or by prying up/out/etc to allow you to get the original panel out. It will most likely be a major PITA, but again it is doable. Just make sure you only do one side at a time until you have the new quarter burned back in to help prevent any tweaks to the unibody. Additional bracing or stays aren't a bad idea to make sure things don't move. You can also measure several point diagonally across the top and the body to use as reference before beginning to help verify your work and that everything is still in the right location.
The other option that many use is to cut the quarter panel either at the leaded seam or below that and splice the quarter panel in at that location rather than do all the work for the area up above with the overlapping metal. Just looking at the pictures you have provided it appears the rust around and just below the leaded seam is mainly surface rust that could be removed, neutralized, and/or easily patched. The other benefit to this is in the area of the quarter glass. Although I am not a hug fan of replacing the quarter that low on the C pillar, doing so and leaving the existing quarter glass and all the trim as is will save you a TON of TIME & WORK!!!
I assume you are installing quarters due to rust in the wheel arches, lower sections, etc. If not, then I would seriously consider patching the quarters as needed, installing a new/used roof skin and call it good. That will allow you to sell off your NOS panels if you want and recoup $$ for other areas of the project. Hope that helps! Good Luck!
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