Wait until you get ready to weld that sucker back in under the car. Depending on you welding skills (and mine are marginal at best when working upside down) I chose to cut mine at the bend that welds to the frame and weld the shock mount and tank support peices to the new trunk floor on a pair of saw horses. We took a ton of measurements to insure it would line back up with the tab I left on the frame and it turned out very well. The aftermarket metal was a PITA to get the mig set right for good penetration without blowing through the thinner metal of the trunk floor.
I'm making sure that the shock tower remains one with the frame, and I'm going to follow Q's advice to drill the replacement trunk floor and weld it from the top. Near as I can figure it, the only thing I'll be doing that does not involve welding directly downwards are the welds at the inner wheelwell. Not sure how I intend to tackle the existing left dropoff though.
Likewise, I intend to weld the gas tank hanger to the shock mount before putting in the trunk floor. If it sags when I'm trying to weld it, I'll put some weight on the trunk floor and jack the hanger temporarily.
What settings did you use, and what MIG are you running? I bought a Hobart 140 for the job, 0.023 wire w/shielding gas, voltage set to its lowest setting ("1") and wire speed @ 30. What trunk floor did you use? The original appeared to be thicker than the frame rails.
-Kurt