For the starter to work, if you bridge the solenoid woth a heany screwdriver or something, it should sent 12 good volts down the light green "by memory" to the starter fields & should spin the motor. So long as you have a heavy red to one side of the solenoid from the battery. Plus a heavy earth from battery to frame. Motor mounts tight for a good earth & brushes under spring pressure. She should spin even without the rest of the system live.
Ok , reading back i see its not charging so must be running. Be good to get the starter operating as could indirectly be to do with why its not charging.

So as you know there`s an added shaft that has the cam lobe and timing advance on it..... And the manual doesn`t even go into how to pull it. It is a hairy Job at least...... I don`t want to mess up the points setting trying to avoid disturbing magneto if I can .Someone mentioned getting on Bike Bandit or similar that sells Yamaha parts . even the manual that has wiring schematic shows pigtail for DT125C says that DT125A/B similar .I`m not comfortable guessing. the only way I got it running was push stating it with fully charged battery. Once its warm kick start will work,but electric starter won`t itll try thats it. It`ll run till the batteries too weak feels like the fuel systems clogging up (which it was but is`nt now....rusty gas tank that i treated there`s still stray crap in )