Hey man I had a similar issue with my bike, wouldn't charge, or at least the charging voltage was super low.
In my case it was one of the alternator coils that fried. The regulator was fed with two phases instead of three. As a result the rectified voltage was about the same as what you have.
Normally, at 3500 rpm, you should get 14V max. 12.5V means it is not charging.
I didn't do anything to find that out, my mechanic did this time, so can't really help ya with the research process.
Good hunting and looking forward to read your findings.
Cheers, ride safe!