That kinda sounds like a 10,000 foot view of the task in question. To qualify - This isn't my first floor project. I have built an entire floor assembly for an S10 project, creating parts that were not available by hand including the mounts to the frame. I have put entire footwell and trunk/cargo areas in G-bodies, including creating unavailable support and body mount rails by hand. The difference here is that those are full framed vehicles and the mounting locations are quite a bit more spacious than the rear mount points for for the second gen. front sub frame. That, and the fact that these are intact and I want to preserve them without creating additional assembly, alignment, or corrosion issues makes this a completely different project. I am concerned that disassembling this welded assembly and re-welding after cleaning, metal prep treating and coating will introduce new issues involving assembly, alignment, or corrosion. Not disassembling them has the potential to not treat all surfaces, allow accumulation of abrasives such as sand or glass bead and trapping paint or other rust preventative coating that could prevent movement of the caged nuts that secure the sub frame, potentially making assembly/alignment difficult while creating a break in the corrosion protection when those nuts break loose from the location where the settled into the coating.
I am not building a show car, this will be driven rain or shine, and probably not babied. I do not put things together without assuming that they will need to be taken apart to maintain, repair or modify and I don't want to build in any problems in those future tasks. I am not looking forward to redesigning that whole area. I am thinking that I should inspect the drivers side before going any farther. If it is not in good condition it would force the issue.