Paul, do you have any teacher buddies that get to work with a CNC mill? You could use your drill-press-sewing-machine method with a CNC mill for spectacular results.
Your project is making me consider selling my race car and doing something silly like build an electric car in place of it... i think it would be cheaper! Hmm... i wonder what sort of lap times i could put in at the sprints with a fully charged battery...
From what I have read the issue with brushed motors and regen comes from brush advancing messing with the efficiency of the regen... but then again, i'm just a forum shmuck that reads the same resources as everyone else.
I must have missed it... what are you doing for current sensing? Are you able to actually sense the current, or are you only able to tell when you've hit the limit. If you can actually sense the current, i would recommend making your pwm controller into a PID current control... if you didn't get that, here's the short version - pedal position would strictly determine current, not pwm duty.
If you don't have current sensing, i recommend it for rev2