Sounds like you need to adjust your pedal to booster rod length. I did a simular upgrade to a 48 1.5 ton and it took quite a bit of adjusting to get everything dialed in. You will need to have some pedal travel after adjusting (meaning don't adjust to the point you only have an inch or so of freeplay) because all of your brake system is under the floor with the heat. Even worse on mine, it's a V-8 truck with an exhaust pipe running rather close to the master set-up. The heat will cause the fluid to expand and "take-up" some of your pedal freeplay.
Good luck,
Scott
