Per your product instructions, it would be the Electrosport BROWN to be extended to key BLACK, right? As long as your new Reg/Rec is getting a proper reading from the switched 12v, it should provide accurate info to charging the battery status. It sounds to me as though the battery recharge is "out of the loop" on your charging system. Make sense?
To verify before you do anything: charge the battery fully. Take a voltage reading at the battery terminals. Probably going to be ~13.8v
Now start the bike, and take readings at 2,500, 4,000 and 5,000. If the voltage is NOT increasing, then the BLACK/BROWN circuit is not communicating to the Reg/Rec/Battery. Fix that link, and you're golden!