The RED wire from your combo Reg/Rec needs to tie to the battery POS terminal. This supplies voltage back to the battery from the stator. The BLACK wire form the Reg/Rec ties into the stock switched 12v service of the bike (usually the key BLACK) to monitor the condition of the battery. This is the "regulator" side of the unit. If the BLACK see that the battery is registering only 11.9v, it allows the Regulator to send voltage back to the battery to restore it full charge. Conversely, if the BLACK sees a "full charge" on the battery, it limits the charge to prevent over-charging.
The issue many people encounter is the BLACK wire tends to have some amount of embedded resistance and therefore measures lower than the battery directly. If that delta is greater than 1.0v you run the risk of over-charging the battery. It is best to insure the Reg/Rec BLACK wire ties into your harness somewhere that reads as close as possible the correct voltage of the battery (as read directly at the battery with a meter). Make sense?
As for your diagram, I don't like it. It is not indicating fuses for the service of the headlight and tail lights. I see a single 20a for the key, thats too high and you have not separated enough circuits. If you blow that 1 fuse, nothing works. As a matter of record, the BLUE wire from your ignition serves coil 1/4 and Yellow serves coil 2/3. And your Stator output harness should be showing a GREEN to connect to your combo Reg/Rec, and the Reg/Rec should have an additional GREEN to chases ground.
Lastly, running a 20a service through your key switch will likely crisp that up pretty quickly. Might want to consider a few relays for the head lights and ignition if you're determined to use a single 20a service. And I hope you've used sufficient gauge wire.