Hi mkent78.
I don't have the ARF version of the SE but I built the kit last year. I don't think the 1/16 gap should be a problem, but I do like your idea of using some foam rubber as a gap filler/cushion. I've done this on some of my other planes where the wing sets into the wing saddle. If you want to do some wood work, you could also just get some 1/16 balsa sheeting and glue it onto the wing root where the gap is most prevalent. Then slowly sand it back down until you get a nice fit. Once that's done, you'd need to re-cover that end section. Might be more work than you'd want to do though. I have noticed some minor scuffs on the fuse of my SE where the wings set against it, but the only time they're visible is when the wings are off, so it doesn't bother me much.

Len