I would think the only way to really preserve all the work you did would be to leave the wiring attached to the structure as much as possible (obviously will need to have cuts though if it's multiple boards, which it sounds like it probably is. Unless by bench work you just meant legs under a single 4x8 sheet, then it would be easy to just leave all the wiring where it is).
Next best thing would be to take very good notes as to where everything is attached and then disconnect, and tag each wire in some way. You will be running all the wires again(re-doing that part of the work), but at least they will all still be the right lengths if you properly identify everything.
If you have the layout in a computer program like RRTrack or SCARM, a good organizational aide would be to print some copies of the track plan and then mark it up with notes as to where everything connects.
Hope this helped, even if not a solid single answer, might give you some things to think about that will help you be successful.