Was the peg / brake pedal in the stock (middle) position and are you on the tall side? If so, the pegs can be adjusted forward, which should give you an entirely different leg / foot / brake pedal geometry. I'm 6' tall, and in the stock position, I had to lift my leg at the hip in order to use the brake pedal. That was very uncomfortable and the reason an RT or ST never really fit me. With the pegs all the way forward on the F3, I can generally pivot my foot at the ankle to engage the brake pedal. It got even better with floorboards. The U-Fit system makes a huge difference when adjusted to your height.
Another option is to get the ISCI hand brake. My wife had one installed a couple years ago on her RT after she broke her foot, and she still uses it a lot.
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