So you've got an electrical issue with a 25 year old motorcycle eh???
First, clean every electrical connection you can find. Not kidding. Disassemble and remove corrosion with fine sandpaper, then coat the connection in dielectric grease. Pay special attention to the ground connections from the battery to the frame.
Second, Start the bike, check battery voltage with rpm at 4000 rpm. Assuming your charging system is working (Approx 14 Volts @ 4000rpm), place your battery on slow charge overnight (8 hours).
Brushless charging systems tend to be quite reliable, I have yet to see one fail - that doesn't make it impossible. What's more likely is a loose connection to one of the many recently serviced components (battery, starter, stator and rectifier). Also, lets not rule out a potentially faulty starter, did you have yours refurbished, buy used or new?
P.s. I can appreciate how bad the phillips fastener is. Blame the British, as they popularized it during the first world war rather than paying a few pennys per pound more for the Robertson screw, a far superior (Canadian) fastener. Get thyself to the Snap on truck and buy a proper #1, 2 and 3 phillips (Snap on, NOT BLUE POINT), yes, there is a difference.