To answer your original question about side sill/rocker panel attachment to the floor. There are spot welds on the floor (horizontal.) That's likely why it won't let go.
Zoom up on the attached pics of the remnants of one of my rocker panels and where it was welded to the floor and you'll see the spot weld locations I drilled out.

Your sequence is probably correct. At the floor to A-pillar joint, there are 4 thicknesses of metal sandwiched there (rocker/side sill, floor, inner cowl panel, and A-pillar) so all those pieces need to be in place before final welding is done.
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Kevin
1951 Chevy 3100 work truck
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1929 Ford pickup restored from the ground up. | 1929 Ford Special Coupe (First car)
Busting rust since the mid-60's
If you're smart enough to take it apart, you darn well better be smart enough to put it back together.