There's one solution given in the RV-3B plans, to remake the flanges. I had to do that a few places for my fuselage. I described it in my VAF blog in
Post #323
and
Post #330.
It seems like this will take gobs of time but it goes surprisingly fast.
Also, if you're going to use glue for holding things in place, I've been using West Systems thickened G/flex, part number K655 (I think) and it works fine. 3M's 2216 is also a good epoxy. In both cases, the joint needs proper skin prep. We don't use the epoxy for filling the entire gap directly but do use it for holding shims in place.
Some people also bond the skins to the airframe as well as riveting them. Let the epoxy cure completely before riveting if you're going to do that, of course. That technique is somewhat complicated and certainly time-consuming but can give good results. It can also make some poor work permanent, just so that you know. If you do this, first bond in the shims and then, after that's cured, bond the skin on. There aren't any real shortcuts. Like I suggested, it's a real time-suction.
Dave