Yep...the second one.
Now remember this is just a plan, and it may not work out as planned, but it would go something like this:
1) Install a new set of pads and spacers on the frame, tacked with glue at the appropriate locations.
2) Install the two inner sills.
3) first loosely bolt the rear tub at the back of the frame and then tack the rear tub to the sills, being extremely carefull to locate it for and aft.
4) Install the new floors, while there is ample room to work...and only tacking at this point.
5) Install the front tub, using bolts and the doors to locate the position for and aft in relation to the B-pillars, and then tacking to the floors and sills.
6) Check all measurements for days, or weeks, till I am completely satisfied with the locations...then final weld the major parts that were already tacked.
7) Finally, install the new outer sills.
I am glad you brought this up, as it is something I have been tossing around in my mind for 11 months, but it's nice to discuss it out loud, as there are likely a lot of other members with better ideas...
And, just so you know, my likely course will be to use a donor tub, and not have to go through all this. It will be a major undertaking, but would give you something at the end that you can really be proud of!
ANother edit! As I rethink it, the sills and floors share the same body bolts, so I think I'd bolt the floors with the sills in step #1. See, it's a very flexible plan...