There is a 3rd option as well. Prime and seal everything while it's apart, even go as far as painting those areas with a "primer" textured and colored paint so it appears to be primer but is actually a nice sealed and painted surface. Then, assemble the car, gap everything so no further bolt adjusting is required, and blow the paint on factory style leaving areas dry and uncovered by body color as they should be. You might not get that look past an O.E. judge as being original, but not many others will pick up on it and it will appear basically "correct".