An electrifying story...

I was taking the alternator cover on/off that I was not fighting the magnet to get the cover on

You'll see if the magnets are damaged / missing, If it was dropped or hit hard sometime in the past this could reduce the magnetism .
Stick a spanner on it and see if it sticks equally all around the rotor.

You could possible have one or two of your three phases out on your Regulator Rectifier box or interconnecting wiring.
which could give you a good Voltage but low charging current. If You could get a clamp type Ammeter (current Amps) you could look into this charging current question more.

Six cells per battery, 2.2 volts per cell, a little higher for Gel batteries so a duff battery less likely, it will charge to over 13 V and settle down at about 12.8

All I DO know right now is that I have to put the battery on a charger after only 5-10 minutes of running

Even if you were running total loss, like a racebike without any charging system, you should have way more than 5-10 mins ...I'd guess nearer an hour.

battery capacity is 14 Ah (Amp hours) igntion and lights is under 14 amps load..

puzzling