Bigpike,I know all about of what your up against on your project, I have done several redo’s for others and myself, One thing that helped me was to take alot pictures and I also used 3M 12174 Wire Marker Tape on all wires to help with reinstall on electrical system,I also made a log/schematic of all wires for any future add-ons or issues.I also updated some of the wires and even a couple fuse panels so it made it easier to add on other items such as interior lighting strips ect.
If doing any wire repairs/add-ons …ALWAYS solder and heat shrink !
This is the time to add any charging ports for cell phones or spot lights,you can find weather proof ports on the internet.
As you may already know ….Use marine grade plywood and carpet glue.
Last but not least…measure twice and cut once !
Looking forward to see the finished project.