If your gaps are good, Cleko fasteners are perfect. The internal springs in those things aren't strong enough to pull together large gaps.
Or you can po boy it and use sheet metal screws.
Either way, you just lightly plug weld or putty the holes shut when you are done.
Clekos are the copper pins in this pic:
http://i39.photobucket.com/albums/e1...6/136ec40b.jpg
As for a primer, I have just been using Rustoleum's Professional clean metal primer for most of the pan and Bloxide weld thru primer for the edges near the welds.