When I painted everything on my civic it was hard to avoid damaging paint under bolts. I used washers for some but that still put a slight dimple in the clear coat. It's only noticeable when the bolts are removed.
Dan, just spent the better part of 2 hours reading thru your post & I must say, I've restored a few classics & moderns myself, but your attention to detail is top notch.
You made that truck look like new. Very nice work.