Now that I figured out what to do, this whole side only took about half an hour.
Removed the cleco's. Used a palm drill and a little bit to clean out each hole. Then injected the sealant, inserted the rivets, and taped them in place. I put all the rivets in and taped them at once.
I then used the giant back rivet plate (18" x 18") so I didn't have to worry about lining everything up, which was a constant issue on the right side.
Rivetet all the rivets at once. Then dabbed sealant on each shop head and spread it to seal around the rivet.
Sealed the filler flange and the tank drain flange and cleco'ed them in place.