OK. So now we have that straight. I had a 2012 for 10 years, let's get started.
Back at the battery. On the positive terminal, there needs to be three, large, red wires connected. Two of them join together into a single terminal connector. One of those wires goes to the starter solenoid and the other goes to the main fuse box under the seat. The third red wire is the positive wire from your voltage regulator. Let's call that the charging wire. Sometimes the charging wire can slip under it all and hide from you and not get put back on. All three wires need connected to the positive battery terminal.
On the negative battery terminal, there needs to be two black wires. Normally they are joined together into a single connector, but I've seen them separated. One is your main ground and the other is the negative wire from your voltage regulator. Both need to be connected to the negative battery terminal.
Back on the red charging wire a few inches forward of the battery, there is a rectangular assembly built into the wire harness itself. Looks strange being there. There's a fuse inside of that. A 60 amp fuse. It's been so long I can't even remember what it looks like, but check that. Can't charge if it's blown.
If all looks good, and I assume you have a multimeter, go back to the regulator and unplug the two-wire harness connector. That's the other end of the wires at the battery. Set your meter for DC voltage and read the two pins in the harness plug. You should have battery voltage. Read the positive wire to chassis ground. You should have battery voltage. if you don't, then there's still an open someplace in the circuit or bad ground. If a bad ground is suspected, the most common place is that main chassis ground under the seat on the right side. Clean it up and tighten it up.
If you're still ok there, plug the two wire connector back in and start up the motor. Check battery terminal voltage, either under the seat or on the battery itself with the engine at 4000RPM. Should have at least 13 - 14 volts DC. Steady or slowly rising, but not dropping. There's no spec in the manual for regulator output voltage with the plug disconnected.
If needed check stator output voltage. Unplug the three wire connector at the regulator, start up the engine. Pins 1 - 2, 2 - 3, and 1 - 3 voltages should all be about 60 volts AC min. Be sure to switch the meter from DC to AC.
If the stator or regulator look out of spec, where did you get the parts? If that all looks good, then you may have a huge current draw that the charging system simply can't keep up with while the bike is running at lower RPMs, because it’s a magneto, not an alternator. The DPS motor comes mind. You can start that search by removing the 40a DPS motor fuse under the seat - fuse position 5 - and see if that improves anything. Enough for now.
