I think its a mighty good question and one deserving of a conversation. I've looked at hundreds of posts, both here and elsewhere, related to Honda-4 builds and haven't run across much at all other than a few photos of tail sections with electrics crammed in. There has been precious little discussion of what can, should, or might be done.
And its not just under the seat either. If a bike is to be built, not restored, then just ripping and tearing into the stock harness - with all the spatial limitations that goes with it - just doesn't seem right.
The way I've thought about it there are really two choices. You can either hide the electrical system (traditional) or you can display it (rare). My thinking is that if you have the ability to put together a pretty as well as functional electrical system then you should do so and make it plain for any one inspecting the bike to see. If you can't do that then hide it. Either way the stock system gives you all the model you need, what you really want to do is relocate stuff. So, what do you want to put where.
First thing is the battery. What do you plan to do for one and where do you plan to put it? The next big part is the starter solenoid, which should be somewhere reasonably close to the battery. The next two big parts are the regulator and the rectifier. Because these two are intimately linked and also have to be connected to the bike's alternator moving them to a remote location will involve splicing wires and increasing their length by a considerable margin. They also have to have air flow, but be protected from splash. The last part to be considered is the flasher unit, but its small and can be put just about anywhere.
Control wiring is problematic. Honda brought everything together in the headlight but there's no good reason for you to do the same. You can make connections anywhere.
Just stuff to think about.
