Picked up tacoma after 3 weeks in shop. Bottom line: ITS THE LIFT KIT.. According to Toyota the shorter body of the regular cab creates a larger angle between the differential and drive shaft (2 degrees) and that is the cause of all the roaring/grinding noise that caused them to completely replace the transmission, transfer case, and rear axle. They said they put 500 lbs. in the bed and the noise completely went away therefore proving that a mere 2 degrees is the difference between smooth and quiet and rough and noisy.
Conclusion: Don't install anything on a Regular Cab 2011 Tacoma that will in any way change the angle the driveshaft makes with the rear differential or you will have the noise problems i described above.. They did say just drive it. No harm. Just ignore the noise and vibration, turn up the radio, etc.
Well friends, i ain't too happy about the outcome of this. My plan is to just move on and accept the fact that this is just the way it is. Don't want to remove the kit cause i like the way it looks, drives and rides. Could always put 500 pounds of shingles in the back and haul that load around.
BTW, I tried the driveshaft flip, it helped with the noise but there were additional vibrations that didn't like. Flipped it back a week later.