All of that above is great info. To add to it:
You can buy from Hondaman (member here) his book (priceless) and he sells a plug and play Blade style fuse panel. No more glass tube fuses. Well worth the small deviation from stock for a stock + upgrade.
You can have the Stator rebuilt if it is bad, Rick's Motorsports in New Hampshire I believe. Oregon Motorcycles in the PacWest is another option. If you're determined to replace the regulator, you can choose a slightly different type of a combo solid state Reg/Rec unit, also sold at these vendors listed above.
As for your harness and headlight bucket: if you're keeping a stock location, stock orientation, then buy a stock harness. The mess behind the headlight won't get any less messy, (no where else to put it) but you can make or buy your "connectors" kits for sub assemblies and then at least you'll know they're in top condition.
If you're willing to deviate slightly from stock on your electrics, then you can dump the fuse panel, the rats nest behind the headlight, and spend about $400 on a MotoGadget M-Unit and M-button and have a super clean, digital controller for your bike. Still keeping the side panel location and stock color scheme for your wiring.
Picture of the M-Button in headlight (this is the entire wiring behind the headlight now)
Picture of the M-Unit that has all the switching, fuses and digital controls of the electrical system
I made my own harness since everything was simplified and substantially reduced. Color-coded electrical for idiots with labels at the M-Unit and M-Button for connections. Simple. Reliable. And modern.