After I spent two hours on Tues night taking a chucking reamer to most of the rivet holes, there was indeed a lot of metal shavings inside the wing so I started with vacuuming that all out.
After vacuuming, I had a few holes to investigate why I couldn’t get a rivet to sit flat. In two cases, there is a rib edge directly underneath the hole, so I filed a small notch in those. In other cases, there’s some structure beneath the hole so I’ll just need to use a shorter rivet.
I spent another two hours carefully lining up the skins, first with the main spar, then with the rear spar, finally with the ribs (effectively, starting with the least flexible part, working my way to the most flexible). I find that getting the skins lined up just right definitely takes some patience. Because the holes are drilled just big enough for the rivet body, a cleco will go into a hole more easily than the rivet, so I found it better to do some initial alignment using rivets in the holes to set the location, then putting clecos in adjacent holes afterwards to clamp the skin in place. I had to use awls to stretch and pull the skin and/or structure underneath into position in some cases .
I also checked alignment of inner and outer jigs to ensure no wing twist; they matched within about 0.1°, which is pretty excellent.
I should be ready to pull all these rivets next time I work on the wing.