You have two different voltages running in your bike- the high-voltage battery pack for the motor, and the old 12V system that runs your lights and horn and such. The question often comes up- how do you ground these systems? More important, how do you ground these safely?
This question comes up because of a few issues. First, in most cases the 12V system on a bike uses the frame as a common ground. Second is the question of where your 12V supply is coming from on your new design.
The options for the 12V supply come down to a separate 12V battery pack- what I did, because it’s simple, and I had some spare batteries around- you can use a battery, or a few if the battery voltage is less than 12V, off your main powerpack- (not a really good idea- it loads batteries unevenly in the pack) or you can use a DC-DC convertor. That is a device that takes your pack voltage and drops it down to 12V.
The DC-DC convertor is probably the best way to go- they’re not too expensive, you only need one voltage to charge, it’s by far a more professional solution… but in any case, you have to watch where your ground is.
On an isolated 12V battery, you can run the standard frame-ground. The 12V system isn’t going to kill anyone, and it is pretty much already in place. On a 12V system that’s part of the high-voltage battery pack, running a frame ground is a seriously dangerous proposition. First, there’s the possibility of part of the high-voltage coming into accidental contact with any part of the frame… especially, through any body parts that happen to be in the vicinity. Second, and a mistake I made, if you don’t wire the 12V and the 72V system using the same ground (I wired the 12V to a battery in the middle of the pack) you get some pretty scary potential differences going on. If my 12V ground has a couple of batteries between it an the high-voltage ground, then the ground-to-ground connection is 48V. Bad mojo. (…and, I might add, as I type this, an incredibly obvious and dumb mistake- but that didn’t stop me from making it…)
On the DC-DC convertors, you get the choice of a cheap one, that is not isolated- that is, there’s a connection between the high-voltage ground and the 12V ground. The more expensive ones are isolated- there’s no connection between the two grounds. Spend the money, get the isolated convertor. With an isolated convertor you can use the standard frame-grounding of your stock 12V system, and it’s safer in general for all the reasons we talked about above. With one that’s not isolated, you always have the potential for shorting your high voltage through your 12V components.
One note about your bike’s stock wiring… I spent a lot of time trying to figure out what I needed and what I didn’t need on the stock wiring harness, and finally I just tossed the whole thing, except for cutting out some of the cooler connectors. Without the ignition system to worry about, your bike’s wiring is pretty simple. You have a ground, and wires running to each light and switch- if you have a wiring diagram for the bike, it’s pretty easy to trace, and reconstruct the parts you need. You get a nice, new harness, you can add things, like a wired ground instead of a frame ground, and, as a side-benefit, you understand what each part is for and how it works.