well the red wire from the preamp is more than likely the battery. I'd bet your next paycheck on it. red to 9v + and black from battery to ring/ground on the output jack.
the pickups wires... looks like the super switch was being under-utilized. i'd bet the red and white were series link and were being sent to ground by that second half they are attached to. nothing appears to be connected to the common on the halves they are connected to.
From what I can see pickups go to the 5 way, 5 way goes to preamp, preamp goes to vol, vol goes to output.
You might want to start over afa the 5 way goes... just desolder everything... then on the side that's connected to the red out wire... connect neck pickup to lugs 543 on one and the bridge pickup to the other side at lugs 123. then the other half of the switch you can wire the two common lugs to ground and wire up the series link from neck to posts 34 and series link from bridge to 23. this will give you bridge humbucker, bridge split, bridge and neck split, neck split, neck humbucker.
I may be going too fast, or too slow... please forgive.