Hi and welcome to TMF.
Never changed a full floor but have done several boot floors. So going on from there remove the boot floor but do make sure your subframe mounts in the heelboard are good.
Once you have the whole of the floor out, everything cleaned up etc offer in the boot floor. Now refit the subframe unless you have a subbie jig made to ensure everything lines up. If all is good now pin the boot floor in place using skin pins, not clecos unless you have the wingnut type. You can at this point still adjust things if required.
Happy with everything, now you can weld the boot floor in place apart from where it attaches to the heelboard and arches. Do keep it pinned in place there though to help prevent any movement.
Rear panel next, the lower section with the hinges, everything down from the bottom of the rear window or the whole rear panel?? The process is the same for all of it, carefully remove what you need to, trim, clean up, offer in new piece. Happy weld in place. Don't forget to leave the quarter panel seams alone until the new quarters are in place.
Now you mention arches, i take it you mean the tubs?? If so you can do these next. Carefully remove the old tub, one side at a time. Now clean up everything then offer in the wheel tub. If its a good fit, pin / clamp in place then weld it to the boot floor. Repeat for the other side. Now again offer up the subframe and weld in the subframe mounting brackets.
Now normally at this point i would be taking off the quarter panels and companion bin. Does the full floor include the heelboard as well?? If so i would now move onto the full floor and go from there. You need access inside the companion bins anyway to be able to attach the inner sills to the inner sill stiffener. So do make sure your bracing is spot on.