Perhaps one of the most misunderstood parts of our braking system. Problems like you are describing can be many, many things. But I think you should check this one first.
You spoke about the rear travel only being a inch or two. Be sure that the piston can FULLY retract in the master cylinder with the peddle released. It sounds as though yours may not be doing this. I don't know what peddle assembly you have but if you have the type where the balance bar is inside a tube then you must be sure that the bar does not bind in the tube when pressure is applied to the brakes.
Either way, the bar must never bind, it needs to always be free to move. Plus the push rod angle should never exceed 5 degrees. Does you peddle go past 'center' when you push it? It shouldn't.
As a note, most manual disc system are designed to have maximum braking with 75 to 100 pounds of force applied to the peddle. For those of us used to power brakes, 100 pounds is a LOT. Put a bath scale up against a wall and press on it until you hit 100 pounds. You will see!
Measure the pressure at each caliper and make sure there is no problem there. You can do the math to see if it about right. Keep up with the bleeding, it can be very trying.
You are not running taller tires than recommended are you?
If all else fails and the brakes are functioning correctly but you are still not happy, you can go to a higher CF pad. Just be aware that many don't get to maximum CF until warm. However, there cold torque could still be above that of the 'cold stopper' type pad.
As in the case of Polymatrix T vs A pads. The T pads are know as the 'cold stopper' where the A pad is considered a race compound that does not work until hot.
BUT, this is a big but
The T compound has a CF of .40 at 100 degrees (cold) and the A compound is .55 at 100 degrees F.!!!! What is often said about race compounds not working at cold tempeture is sort of true. The fact is that they don't work as well. The A compound CF will raise to .7 when hot (one hard stop is enough). The difference between .55 and .7 is huge. If the brake system was designed for .55 and you heat them up to .7 then you end up with a system that will lock up easier and you will have to carefully modulate your braking pressure. If you design the system for .7 and you have a .55 pad cold, you are not going to stop at the full potention of the car until the pads come up to temperature. Hence the saying about race pads not working until hot even though technically they often work better than softer compounds when cold!
Phew!
Happy trial braking!
Rick