I don't understand what you mean by "lay out" the wiring. If all the original wiring is missing, then it's really easy - you don't even have to trace wires! Just hook up the coin switches to the Jamma harness, and the coin counter. Lights need to be wired up to the power supply - decide what kind of bulb you want to use, if you use normal 6 volt bulbs you can wire them in parallel and hook it right up to the power supply. Lots of people use the -5v terminal on the power supply to power coin door lamps because it's so rarely used. Or, if the game's transformer has a winding for coin door lamps, you can use that. It's a good idea to fuse this line though, since you don't want a shorted bulb socket to take out your power supply or burn wiring.
-Ian