Sorry you’re having problems with your motorcycle.
This one is probably easier to solve. I don’t know how comfortable you are with electronics. Do you have a voltmeter?
First thing to understand is how that red light on the on instrument panel works. The light does not show anything to do with whether the system is charging or not. The light shows us when the charging system voltage is too low. By the time the light comes on you are already stuck somewhere.
The problem with this method is if you have a new battery, with a full charge, the light will not come on until it’s drained down. I think the light comes on at 10 volts.
As you already discovered, you can charge the battery and it will run like everything is normal until the voltage is under 10 volts again.
In summary: the light will not indicate a bad charging system until the battery is almost dead.
In my experience, the stator is bad. I have not seen a bad voltage regulator unless someone had a wiring problem that shorted the regulator.
If you want to check the stator:
One of the connectors on the voltage regulator has three wires and goes to the top-left side of the engine. That is the stator output.
Set a voltmeter to measure AC voltage. Start the motorcycle. Using the voltmeter, measure between two pairs of wires at a time (three combinations). The meter should indicate more than 20v at 2000 RPM. The number doesn’t have to be exact. This is usually good or it measures zero because the stator shorted.
I did have a partially shorted winding on one of my bikes. It passed this test but still could not charge the battery under a load. That’s why I’m cautious about trusting simple measurements. In truth the windings should be tested under a load but that is more complicated to do.
If you want to be sure, replace both the stator and the regulator. There are only two components and one (or both) of them is bad. As I wrote above: I have not seen a bad regulator on a super x yet. On my old Honda Gold Wing both components failed at the same time so some bikes do have those failures.
The short version (if you don’t want to do the measurements): the stator is bad.
