Make sure you run a robust ground cable between the alternator body (one of the mounting bolts is most convenient) and the engine. Or a common grounding area that the engine is grounded to.
And of course, make sure that grounding the engine to the body is a prime part of your grounding theme.
With all the painting and powder coating going on, I'd just make sure that bonding everything (or at least most things) together is a good practice. Because they're no longer going to be contacting at normally conducting surfaces.
Presumably the body is going to paint at some point too? If so, it becomes just as necessary sometimes, to bond body panels together with extra straps or wires, to make sure that they are all part of the system.
After all, it doesn't do you any good to ground the headlights and turn signals to the core support, when it's no longer getting good contact with the rest of the body. Especially the few grounded panels that there normally are.
Keep it in mind when welding any new panels, or painting any old ones, where they need a good connection. Like the windshield frame, as another example.
Paul