The responses are all over the map here. LOTS of opinions.
I don't see how pads could get glazed if they never got hot enough to stop the car.
When a "custom" situation like this gives poor results, maybe a wise move is to mimic a setup that the factory used. Once you have a matched set of components, you have a better chance of success.
Here is what seems wrong from my point of view:
Wrong type of master cylinder for the application.
Lack of proper front/rear proportioning.
Again, the OP has not given all the information. Maybe I missed it?
Vehicle, brake size, caliper bore size, master cylinder adapter size and type, brake pedal pushrod length as compared to the original. Again, once you deviate from a factory setup, every single component results in a "variable" that can cause trouble if it is not correct for your application.
Trying to help with such little information is not easy. If you want help, you need to give more details.
Are you listening?