Body/top alignment/repair sequence advice?

[Tumbleweed1C4]

My Blazer is missing the Torsion boxes, and I have to repair the floor and rockers too. I went ahead and ordered the parts for the passenger side, and attempted to get body mount set from GMC Paul, (which they do not carry anymore btw). I think my tub alignment is being held in place by a six point rollcage put in by PO, and I want to remove it. I can't replace the body mounts or rebuild the torsion boxes without removing it. I tried to put the hardtop on to hold the pillar alignment in preparation for tackling this mess, but its been off for awhile and bolt holes do not line up. bed rail bolt holes are about 1/4-1/2 forward of single wall top holes when the top is bolted in place at the windshield. Any tips on how to fix this? My doors are not in alignment to begin with, so how worried do I need to be about things moving if they are not in alignment to begin with? I am not even sure I am not going to take the bedsides off to repair rust in floor at back corners. Should I repair floor and rockers and get all that aligned before removing bedsides? Anything I can do while I wait to get a set of body mounts?
The pics show condition of body mounts, the rollbar attachment to floor, and the relationship of hardtop to bedsides right now.