One of the tricks we suggest for just such problem areas while you have things torn apart, is to thin some bulk Zero Rust, pour it into the affected area and let it "seep" into all the cracks and crevices, pouring off the excess into a catch basin for reuse. Thinning helps put our paint's solids in contact with the steel that it wouldn't otherwise make contact with in the more concentrated form.
Seams, pinch welds and the like are always a DIYer's nightmare, but with a little work, you can at least get some rust inhibitor on that steel to gain rust protection, then use your seam sealer.
HTH
WK Irish
