Thank you all for the insight and recomendations.
I was able to screw the floor support to the floor panel and install the rocker panel extension with some effort so I think I have a plan of attack. I still need to re-fit the upper portion of the inner cowl but I think once that is in place I will remove the bracing and check the door fit. The panels reinstalled seemed to fit much better, or at least more consistantly this time.
Once I check fit the door I will reinstall the brace and remove all the panels again to drill holes for the plug welds and prep the overlap surfaces prior to "final" screwed assembly prior to welding. Depnding on how the initial door fitment goes I may recheck the door fit one last time before doing any welding.
The good news is the weather is finally starting to get warm enough that it is reasonable to work in the unheated space.
