Initially we had hoped to use drum brakes on all 3 wheels. Drum brakes remove the brake pads from the braking surface under normal operation. Disc brakes leave the pads just riding on the braking surface adding a small (or large) amount to the rolling resistance. We also another discussions about other bizarre braking options which may have worked but would have been frowned upon by the engineeringly educated.
Due to problems finding appropriate wheels and our reluctance to manufacture our own, we ended up buying front wheels with disc brakes. Our tests suggest that if spin the wheel after using the brakes, the pads will gradually be pushed back so that they only touch the braking surface at the point of rotation where the disc is most deformed. This is potentially an added benefit of using dodgy second hand motorcycle wheels.
Once we start doing some more road testing we will investigate whether there is substantial resistance from the disc brakes and decide whether we need to manufacture a mechanism to pull the pads back off the discs.
For the braking controls we eventually decided on a brake pedal for the front brakes. The brake pedal is connected by a lever to a master cylinder from a caravan that is connected via steel tubing to a flexible cable that runs down to the brake calipers.
The rear brake is operated by a car hand brake lever. This is attached to a cable which is plumbed back to the drum brake lever on the rear wheel.