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)

I read a post on another website that some brakes are self adjusting and therefore should be driven in reverse and then have brakes applied.
I did the same . drove in reverse barking heard making the abs turn on a couple of times.
Interestingly the pedal did become a little better but not really where I want it to be. after about half an hour of driving however the pedal went back to the long travel where it had started from.
My question: why did the pedal feel change when the method of driving in reverse while braking was applied ?

__________________
Whether you think you can or cannot, Either way you're right!. by Henry Ford.

If the car stops even with extra leg power the pads and calipers are probably working OK and the master cylinder is delivering fluid to the brakes. Check the vacuum at the booster if OK check the venting valve on the brake pedal side of the booster, under the dash. Check the vacuum source on the intake manifould.
Sounds to me like your leg needs some help from the booster.

air in the lines maybe?

Benz300, that only applies to drum brakes with self adjusters.............
William Rogers........

well.. the air scenerio should 'hopefully' not be applicable since I've bled the brakes 4 times. however theres an interesting topic where they say that cars with ABS sometimes have air trapped in the ABS system. so it could potentially be the case that when I drive the car in reverse and brake heard engaging ABS, the air frm the ABS is travelling down to the callipers and in turn helping a firmer pedal feel. I'll get the brakes beld again while the pedal is better after ABS has been egaged a couple of times.
More over it seems like a soft pedal is a common complain with lexus owners. one of the things people have done are to change the brake likes to stainless steel lines. I've ordered the goodridge SS lines and will have the tech put them on too. let's see how that helps out the situation.
thanks again for everyone's input. I'll keep you guys posted.

__________________
Whether you think you can or cannot, Either way you're right!. by Henry Ford.