Where does your pedal sit as it is installed without any fluid in the system? The return spring pressures in the MC and booster are going to be at their furthest extension even without any fluid.
My first thought is that the physical location of your pedal or the push rod needs to be adjusted (This assumes you have the system properly bled and residual valves place for the low mounted MC, which it sound like you have) So, that static position needs to be physically positioned even before hydraulics come into play.
You may also consider the bore of the master cylinder. A small bore will allow easy pressure but will need a longer stroke to push enough fluid to engage the pads on the rotors. A larger bore pushes more fluid with shorter stroke but very difficult to press. Since you are running a booster, you can go with a larger bore MC.
Balance the physical position of the pedal with the MC stroke needed to engage the brakes and you should get dialed in.