Finish the painting, first - it's likely that the paint build-up will fill your holes without extra effort. Some partially dried paint gobs could do it, too. Any remaining holes could be caulked after the coating is dried. If it's a color matching thing, then a final paint coat over the seam after the caulk is dry probably won't be disastrous, even if it eventually fails.

Glad your skinning went well! How do you like that 14oz polyester? I looked at it, but went with lighter stuff in the end.

Dave Gentry