Yes getting the sill out is a big step and project. Try and think of the body as flexing and twisting other than sliding, but yes the tub will slid also. When you stand back now, you can see that the inner sill removal is going to come out like pulling a tooth. So Be less intrusive as you can, but grind and drill out everything that has to be moved out of the way. To get started you can go onto the kick panel under the dash and undo the spot welds like on the outer sill. If things get too floppy, you can run some screw into the 2 pieces to hold things in place for a while. I suggest tipping the tub up on the frame maybe 8 inches; you can put some wire through the holes of the tub to the body mounts on the frame on adjacent side to keep the tub from sliding off the frame. I say this because I could move the tub around that way plus keep an eye on the mounting points. You mention you want to use or keep the floors in or reuse them and that sounds like something I would do, but I am not sure if it is way to go, maybe.
There are many ways to do this; I did not have the room to pull the tub and cut out the inner sill with the tub off the frame, so maybe that would be better for you I do not know.
For now, I would not enlarge any holes because the new sills are going change everything a little. The car panels like the front fenders bolt to the sill and the little rear quarter panel laps over and welds to the sill under by the B post on the inside and outside, so the most the cars is inter-woven back on the sill, so getting the sill back into its new home helps align the placement of the sill, and requires a lot of fiddling, so things are going to be a little different, so I would suggest not enlarging any holes for now. Like John maintained the A and B post get welded later for the precise door opening. You got this; it is not too difficult.
Steve