The sills are very important structurally when lifting the body as is alignment of the sills to the bottom of the doors. Because of this I chose to change out the inner and outer sills with the body on the frame before lifting the body, provided you had good to fair panel/door alignment.
The floors aren't as crucial with the exception that the floor should be at the same height as before and if not that can be fixed via shimming, whereas no amount of shimming will fix bad sill positioning.
Also, it appears much simpler to cut out/clean up and tack the floors in place prior to dropping it back on the frame. This is the rational I followed and so far so good. I've replaced the sills and aft b pillars and am moving on to the floors. I check all panel alignment before locking the sills in place.
Lastly make sure you brace the body at the top of the doors prior to lifting it, I also braced it right by the sill too. A point of note on bracing the car, do this when it is sitting on the wheels because we all know how flexible the frames are.
Good Luck
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