Designing a BLDC generator
You're unlikely to achieve losses less than about 30-40% total, with around 10-15% just in electrical losses through rectification and DC-DC conversion.
This would require 37 V @ 46 A to 12 V @ 125 A conversion, which would be a fairly major DC-DC conversion project all on it's own. 

You may have more success (simpler design) using something like a 4S BLDC such as this one from Hobbyking with synchronous rectifiers and voltage to speed control.

A simple speed control algorithm may be to set a single voltage control point such as 13.8 V (Lead Acid batteries for example) which triggers Idle for your motor.
This would hunt at the trigger point so you could be creative to solve that: 


Start at Idle, test battery voltage
Based on battery set full rate charge for a time (say 3 minutes), start to accumulate number of charge periods in you MCU. 
At period end, lower speed (but not to idle) and measure battery voltage, decide on next period to charge if voltage at limit, then idle for a defined rest period ...then go to 1.


You could of course measure the charge current and control that, but that would be a bit more complex to implement. 

One other thought is to measure the charge power (indirectly) and control that.
For example, if the coupling between the motor and BLDC was a spring coupling with two sensor points, one on the motor and one on the BLDC shaft, you get a measure of the power drawn from the BLDC by the twist in the coupling. ...just a thought.