If I'm understanding you, the M/C and booster assembly is backwards- i.e. the booster is facing away from the pedal.
If the correct set-up isn't available for whatever reason, and there are no other mods that could be made to the existing set-up to make it work w/the M/C correctly positioned, it could
be done mechanically if you used linkages and bell cranks, but it'll take a few tries to get it sorted out. Your best bet might be to adapt it to hydraulic opreation between the pedal and the brake booster, if I understand the layout.
What I'm talking about uses a small hydraulic cylinder to actuate a ram that can be mounted where ever it's needed. The basic components are shown below, these are from CNC Brakes, and are originally intended for use w/a clutch:
Problem w/all that is you'd need to adapt it to your pedal, etc. Possibly a different rod as mentioned above could work, does your deal look like: