Basically what you want is to get welting installed with minimal damage and maximum ease. When building my cabriolet a few years back, using repro steel fenders, I installed and removed the fenders multiple times as I was fitting everything. Each time there is some difficulty getting the fenders away from the fender bolts/studs welded to the body. As you seemed to be saying, the bolt holes in the fender might not be in the exact proper location. A fair amount of twisting and pulling can be used to move the fenders a few threads away from the body. Over a period of several removals and installations, I enlarged the fender holes, remembering that the fender washers will cover a lot of enlarged holes. If you don’t have the standard fender washers, buy some as they are available at most hardware stores. Using wood wedges as previously suggested will help you make progress in pulling the fenders off the bolts/studs.
Welting can probably be installed without full removal of the fenders, but such removal will ease the fitting of the welting. Because the surfaces have complex curves, welting may need cutting of the ‘flap’ at varying intervals to get a tight to the body fit. You also will want to cut a wider slot in the ‘flap’ where the welting contacts with the studs. Once you have the welting fitted and are reinstalling the fender for a final time, it may seem the welting is too loose sitting in the gap between the body and fender. Don’t worry as the gap pretty much disappears as the fender is tightened up against the body, but you need to tighten the bolts slowly and keep pushing the welting bead into it’s proper position as you tighten the bolts.
Good luck with the job, and be patient, but unafraid to use a bit of force to twist, push, and pull the fenders off the body bolts.