Tub/Fender/Top alignment questions (w/Pics!)

[67Steven]

I am getting ready to replace both the driver and passenger side inner and outer rockers and a small section of floor ( I think I will use the truck floor section as I read it is a better piece)

I want to put the top on to keep the windshield frame stable for this operation, but do not have the bed side seal. Can I just bolt the top down bare, or should I use a washer or other to space it properly- does it matter?

I changed the 4 tires that are all different diameter out for a spare set of GM rollers I had to get the chassis closer to level:



Here is how the doors fit now. It's hard to see, but they line up very nice:







The fender to door gap is what I have an issue with:





I know that I can shim the body mounts up to alleviate the gap, but how much can I or should I shim (how much is too much?) I know they are not torqued down, should I bolt the top on first, then the body mounts?

The body mounts now