The stator windings, behind the flywheel, would be the first thing I looked at next. Still possible the reg/rec is faulty or badly earthed (grounded) though.
Run the motor and put a volt meter across the battery. It should show a steady reading (approx 14V) while the motor's running. Blip the throttle, and it should still read steady. Run it without the lights on so there is minimal load. If it looks fine, a good test is to press the "pass" button to flash the headlight. That creates a sudden drain on the charging system and will often show up a bad battery or reg/rec.
Erratic electrics can usually be traced to a bad battery, bad reg/rec, bad earth, or bad connection. Very rare for the electronics (i.e. the PGM) to fail on the NSR unless it's not been looked after very well.
If it was running and all you've done is replaced the battery (with a definitely known good one), then I would be looking for a loose connection.
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Andy.
NSR-WORLD.COM
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