Have done several... Not all TR's, tho.
Depending on the body design, I x brace in the doors, A to B pillars, etc, to reduce body flex. ESPECIALLY, if you are going to use a roto...
The body comes off the frame for this to be easier to do. [Now is the time to repair, clean, paint at least the bottom.]
Once the frame is out, everything is level and well supported, the plasma torch comes out. We cut as close to the pinch welds in all areas to be removed. This allows for spot weld grinding, removal of the "scraps".
The new pan is prepped by cleaning the pinch weld flanges, cleaning and scuffing the pan surfaces, prime/paint as desired. Remember there's a difference between REAL E-coat, and cheapo black primer, when you do the prep. We then use a hand punch to punch spot weld holes in the pan flanges.
The frame has all the work done to it, B4 reinstalling.
The new pan is then mounted, [w/ new bushings], on the frame, slid under the body, level/squared. [Body HAS to be level and square, too.] When you see the pinch weld flanges fitting correctly, U are pretty much GTG.
I use small, self drilling screws, to attach the pan to the body pinch weld flanges.
Once it is all measured twice, checked 4 times, I spot weld some of the easy to get to weld holes.
Not a bad idea to check door fit, B4 final welding. [Remember, there are new body mounts involved.]
I use weld thru primer, and a drill bit that matches the spot weld hole punch. The drill has been ground flat, so it will remove the weld thru primer for a cleaner weld. [Ya, I know anal, ain't it??!]

If the toe board is rusty above the joint, install the new floor, then replace the toe area.
I skip weld the toe board joint from the inside.
Seam seal all the joints..[Use paintable sealer]
Main tool list:
Plasma cutter
110V MIG w/ .023 wire.
Makita drill.
Cut off grinder. [Use on most of the spot welds.]
One last thing........I always buy the pan w/ the inner rockers and braces already installed. U will be glad you did!
Spot weld cutter. Don't waste $$ on the cheapos!
A large supply of Vicegrip clamps of various configs.