You just modified this bike, if I read your post correctly. You may be having a grounding problem, or some wiring harness issues. Particularly, on the 350/400, the alternator wires have bullet connections under the left engine cover: these are a common problem area.
The key question is: what modified electrical stuff did you add? The 350 has a low output alternator that is fine with the stock electrical components if the harness connectors and grounding are OK. Add a high wattage headlamp, electronic ignition, etc etc... and the alternator can not produce enough electrical power to get the voltage up to "full charge" level.
You have about 120 watts of power available from the alternator (I did not look up the actual number, but that's close).
The wattage drawn by a load changes with voltage, but it is exponential. Double the voltage and you draw four times the power. It doesn't sound like a big difference between 12.5V and 14.5V, but it's 35% more wattage load from the electrical devices.
The regulator limits the system voltage at about 14.5V but with too much load it never gets that high: the system voltage balances at whatever voltage the alternator, at 100% output, can push into the load. You can not add much load at all to a 350 before getting exactly the symptoms you describe.