That sounds like your PTO clutch is heating up and shorting out internally. Out of curiosity, use the resistance setting on your meter to get a measure of the clutch coil's resistance. To do it, unplug the wires connected to the clutch, set your meter to the resistance setting (ohms) and touch the leads to the coil wires. I'd expect a fairly low reading, perhaps 4-20 ohms. Run it until its hot and draining again, then immediately re-check the clutch coil. I expect you'll have a LOWER reading than before. A lower reading would indicate that the coil inside is shorting across several windings and it will draw more current than it should, thus causing charging system issues and possibly blown fuses.