Look, dude. In the end you're gonna do what you want to do. No one can stop you, but we can at least give you our own opinions and they're probably based on similar experiences we've had at your age and/or experience level.
Here's my opinion: Stop. Just stop. Stop with the modification plans, like, at all. Don't go changing the electrical system, handlebars, switches, lights, gauges, seat, or anything else that isn't broken.
Get your endorsement. Get the bike running and in street-worthy condition with the original configuration. Then just ride it. Get acquainted with it for a good long time. Learn the ins & outs, figure out its quirks, get a feel for its strengths and weaknesses. And then ride it more.
We've all been there, or at least I have. Grande ideas on how to make your bike/car/whatever your own unique thing. They're great and admirable ideas, but also have a huge potential to turn into a non-functional money pit. And if it ever reaches a state of 'complete' (which it won't), you'll probably have a bike that both looks and feels like just about every other cafe'd project on the road. And I can nearly guarantee that you will get way more turned heads with a properly done up stock CB650.