There's no hero to it. Just some burn marks from tinkering with them
First, understand the m-unit has essentially nothing to do with charging. While folks who use modern Reg/Recs do connect the BLACK wire to LOCK or AUX, that is purely for monitoring the 12v switched power status. Thats it.
To your question, I suspect strongly that you have a ground issue (not with the m-unit). If the m-unit is misbehaving, the input side lights will flash steady, then reset, then function as long as there is no further fault. (Not that you can see these while riding mind you, but it does work that way). Also, the horn will typically beep 2x at you when the m-unit detects low voltage, so again, I didn't see you notice that. So that leads to a short, probably on the ground side.
Scottly gave some great diagnostics in this thread that you should also follow:
http://forums.sohc4.net/index.php/topic,157625.msg1829287.html#msg1829287But your battery voltage is suspect to begin with, so that should be fully recharged before attempting to accurately diagnose a charging issue. But you can investigate ground issues by checking resistance to ground from the battery NEG to different areas on the frame, plus any device grounds (including the m-unit) to chassis as well. You want clean, shiny, bare metal contact for your grounds. No paint, no powder coat, no corrosion between the ring terminal and metal.
That will give you something to do while your battery recharges