You asked about a bare-bones harness then mention idiot lights, gauges, turn signals, etc? AND want to use the wrong switches? OK... To wire the thing start with stuff that allows you to get the bike running... start with the AC lines from your stator to the regulator and rectifier.
There are a couple kinds of stator (generators) on a 650. I am not sure which you have. Does it have three yellow wires? Do you have a combined regulator/rectifier or separate? The wiring for this stuff is critical and you should first design this wiring (lay it out) and the fuse box. Then a wire will go from your fuse box to an ignition switch of some sort.
Out of the ignition switch, you will have a number of "legs". One of the legs will go to the rear tail light directly and one to the right switch where it will run through the kill switch. This line will provide power to the coils eventually. Last, there will be yet another line that may or may not run through the right switch depending on whether you have an on/off switch there for the headlight. This line will SPLIT and run back through the fuse box through the two smaller fuses there and become two fused/switched subcircuits. The color is generally BLUE for one and BROWN for the other. The blue will handle the headlight and brake light (not the running light in the brake which was the red wire directly off the ignition switch). The BROWN circuit will handle your horn, the turn signals and provide feedback voltage for the regulator or regulator/rectifier.
On a Kaw, the main ground is generally on the engine cases above the kick start. If you trace this ground it goes into the main harness and snakes out through the engine bike and also hooks to the NEG terminal on the battery.
There are generally two sub harnesses in front and one in back. The front will consist of the idiot light subharness where connections run from various switches to the idiot lights; like the neutral light and oil light and sometimes a rear brake light. The other subharness will connect the wires from the headlight (hi beam, lo beam and ground to the headlight). The rear sub harness plugs into the main harness and comess off the brake light and rear turn signals.
You don't need a "bare bones" harenss as you have EVERYTHING hooked up with the exception of your starter and the only real "mod" is that you have moved the ignition switch. Again, I recommend you buy a stock ignition switch and put it where it was orignally and use a STOCK wiring harness and STOCK handlebar switches... I know that you didn't want to hear this but if I were to draw a new wiring harness for you it would look like the old one only have the new switches hacked in with longer wires for the relocation of the ignition switch and hacks to accomodate the different functions on the handlebar switches.
