Mike,
I have the other setup, and my pedals are still mismatched as far as height from the floor. I believe you can correct that on your truck by using an adjustable rod and clevis from the force reversing lever to the master cylinder.
Basically when you step on the brake pedal, it sets up a pulling force. The pedal has a rod and clevis that is connected to a lever that is mounted to the frame That lever has another rod and clevis that now uses a pushing force to the MC. I believe there were also some pedal bumpers that were originally used which acted as a stop under the floor. Those have probably long since deteriorated, contributing to your problem.
John
