So at 25A average and 50 peak, you're pulling roughly 1100 and 2200 watts. That seems really excessive to me, as lots of rides do 30 mph with 500W motors. I was thinking of trying a 250W dewalt 12v at 18-24 for my roadie. I know it'll only be assist, buy hey, I need the exercise and I've got it and bunches of liion laptop batts.
But seriously, I looked over Matt's site you linked - hes calculated at 290 watts average in his last update, if I figger right (14.5 W*hr/mile * 20 miles/hr = 290W). and he's geared down pretty good to keep motor speed up, with a bit of a fan at motor speed if I scanned it right.
I like those motors, really efficient, but the RC guys don't post torque-power-speed curves like the industrials I 'm used to dealing with. DC motor current draw is highest at start and drops with rpm. Lots of the high current at start goes to heat - maybe you're off on the motor speed at cruise?
On the sync issue, you're using backEMF for speed sensing I think. Most motors tied firmly to moving machinery where inertia controls speed and the controller follows and adjust use hall sensors or encoders to track the actual rpm. Was the ESC guy saying you're adjusted as far as possible on the backemf following?
I know the new backemf controllers are way better than before, but maybe they're not there yet. Matt seems convinced they are, yet needs a slipper clutch to keep from breaking parts. He's a sharp guy, so that tells me it's more than just being throttle happy. If the throttle was too touchy, he'd reprogram it.