I am also doing a lot of metal replacement in my 69 coupe(trunk floor, wheel houses,framerails, quarters and full floor)
I have finished welding in new toeboards and drivers inner rocker
and am getting ready to put in the floor. I have my shell sitting
on a wheeled frame supporting the underside of the rockers. My plans are to leave the old wheelhouses,quarters and tailpan intact for now.
I will weld a brace across the tailpan, then run supports from it to my shop floor. I will cut out some of the trunk floor behind the back seat as well as the front foot or so of the frame rails so I can put my floor pan in from underneath.
After welding in the floor to the rockers and toeboards for structural stability I was going to cut ot the rest of the trunk floor and frame-rails. From here I will replace the inner fenderwells, put full trunk in from underneath, and then new framerails. I would then cut out the old quarters and do the outer wheelwell and install the new quarter (one side at a time).
Now for the disclaimer, I have never done a project this indepth before either (quarters and doorskins mostly so far)so any advice would be appreciated.
If you like I will try and get a few photo's and will
give you updates on how it comes together.