Hi Andy,
I use exactly the same system as you describe, a scooter motor driving via chains and sprockets (3/8th's pitch).
The system is all as it came from the scooter, with no mod's to the electronic brake, and it has functioned fine for 18 months now without a hitch.
I have made provision for a separate brake system using 'mini-moto' calipers and cables, but haven't fitted it as yet. I'm going to wait until Harvey (the grandson) gets a little older, and can grasp the concept of a two pedal system.
Until then, the electric brake is more than adequate, stopping the car in it's own length from full speed (6 mph).
Full details are on my build website (click the 'globe' icon under my username), or my build thread 'Hi To All' in the 'Toylander 2' section.
I wouldn't worry too much at present, just get it finished, and modify it later, that's what winter is for!
Regards,
Mark.