The sheet metal was done in the following order:

Cowl Side Panel
Firewall patches
Inner rocker (not available so 16 gauge sheet metal was cut to fit)
Toe Boards
Floor Pans
Wheelhouse patches
Rear (underseat) Pans

I found it easiest to plug weld to the frame members first and then to the inner rocker, and then lastly the overlaps. After all the plug weld holes were welded up, the entire perimeter of the panel was tacked every 1" working my way around the panel. Then tacks every 1/2" to get a good tight fit. With the thin sheet metal, it is imperative that no gap is present between the old and new metal. Any gap whatsoever will result in blow through and big globs that will need to be ground and re-welded later. Finally, I seal welded the perimeter, welding about half an inch at a time and then back-stepping in order to not warp the floor pans. I don't know if it is necessary to seal weld the panels inside and out, but the advice I was given was that it was best to do so as the floor is part of the structural integrity of the unit body, so it should be as strong as possible. Also I believe that at least the outside should be seal welded to prevent entry of dirt and moisture. Of course, I didn't start out that way so the first panels I welded in weren't too pretty! After welding I ground the welds down close to the metal surface.

I used #8 machine screws with flat washers and nuts to pull the panels together where necessary. This enabled me to get a tack in on areas that didn't want to close up. After the welding was completed, the screws were removed and the holes plug welded. Using a piece of thin copper as a backer kept the heat down and gave the filler metal a foundation. The steel will not stick to the copper due to the difference in melting temperature. This also has the benefit of essentially adding plug welds between the overlaps.

The rest of the right side floor.

Left Rear Floor. Again, I considered removing only the rotted area and putting in a small patch, but learned my lesson on the front left pan. I purchased rear floor patches and cut the majority out.

The left rear floor removed. There is a lot of mud and rust on top of the rear torque box so it is a good thing that the area was removed so it can be cleaned.

Same area after cleaning. Note that the rear panel (behind the seat back) will require a patch before the floor can be repaired. You can also see the patch on the inner wheelhouse bottom.