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.
Many thanks, I managed to get the remnants of the sill out from under the floor with a little 'persuasion'. There were indeed 2-3 spots on the horizontal which weren't massively obvious. Still cannot find any welding instructions for the sill but at least it is out now and I will know better when tackling the same on the passenger side. Managed to hammer/dolly the flange into a nice flat edge ready for the new sill but only after I resolve the rear corner and bottom of the B pillar which are both a combination of 1/2" bondo, 2 pounds of rust and little else!
Onwards and upwards!