You mentioned this in another thread (forgot which one) and I provided a word of caution with adjusting the parking brake to only 3 clicks, but here's maybe a better explanation of what could be occurring.
Yes, you are correct that the brake systems are completely separate. As the LC200 has rear disc brakes (unlike the 80-series with rear drum brakes, the emergency brake s actually mounted inside of the rear rotor, known as an auxiliary drum brake.
On four-wheel disc brake systems that have "mini-drums" inside the rear rotors, the parking brake works like a conventional drum brake. Pulling on the cable forces the shoes outward against the drum to lock the wheel. But unlike a full-sized drum brake, there's no self-adjuster mechanism for the star wheel to compensate for shoe wear because one isn't needed. The only time the parking brake is applied is when the vehicle is at rest so shoe wear is virtually nonexistent. The shoes should last the life of the vehicle -- unless the parking brake is binding and causing them to drag. The thickness of the shoe linings doesn't really matter as long as there is enough lining left to hold the car on an incline with normal cable travel.
What this means is that most likely you have adjusted the screw for the hand brake so tightly that your auxiliary brake is binding. If the binding is too tight, you may have worn the brake out and really should have it looked at by a dealership. With 3 clicks to lock, I cannot possibly see how you are not driving with it bound to some degree. As this brake is only designed to be used in emergencies or to hold the vehicle stationary when parked, it's not designed for any kind of friction/heat while driving. It wouldn't take long to burn it up.
The most likely reason you are experience "low peddle travel" is because, when you first adjusted the e-brake (mistake IMHO) to only 3 clicks, you were driving all the time with the drum brake bound (not good). As the e-brake is now shot, you now don't experience the "benefit" of having the constant braking force and are thus experiencing "normal" brake performance.
Not sure what your experience driving trucks are, but truck brakes are not nearly as hydraulically assisted as sedan brakes (not to mention the added weight) and thus require much more pressure and travel to activate.
If your handbrake was set to 3-clicks, I'd be very surprised if you didn't burn the system out.
Like I said before, mine is set to 8-9 clicks. I had the dealership check, and even at 1 click it is partially binding. It's going to take 8-9 clicks of force to lock this massive a vehicle.
I'd highly recommend never touching the brakes unless you know exactly what you are doing (I'd never touch mine). Take it to the dealership and have them examine the system carefully...
