I agree with you. It sounds to me that the Master Cylinder is not working properly. Is the Booster getting the correct vacuum to it? No leaks?
Also, just another thought. You say that the Booster was changed. If I recall correctly, the brake pedal goes to a little bar that when you brake it goes into the booster that "boosts" the pressure to activate the master cylinder to brake. Now, I wonder since you changed the booster, was everything put together correctly, mainly this little bar. I do not know if it has threads on it that you can adjust?
Maybe, just maybe, the dealer did not do a good job of putting everything back together again and this little bar is not making enough contact or correct contact to cause efficient braking. Hence, you have to push the pedal almost to the floor to brake the car. This scenario is only valid if it is true that the master Cylinder is good!
Insanity: doing the same thing over and over again and expecting different results.
2006 - Suzuki Gran Vitara (2.0 L fully equipped) Like this car so far except for trying to put on the seatbelt.
1988 - 190e - 2.3L - 172K miles (It now belongs to the exwife)
1999 - Chevy Blazer LS Fully Equiped - killed it June 2006
2001 - Honda Civic EX - 68K miles (sold June 2004)
1963 - 220S - Dual Carb 6 cyl. (sold)
1994 - Yamaha WaveRaider (fun to ride)