"one [truck] with the solid black flywheel, seems to be turning faster. The back, one with the timing tape, is still turning when I lift up slightly off of track but doesn't seem to be as fast as front."
That itself is not abnormal behavior, at least when the trucks aren't on the track -- all PS2 and PS3 engines behave that way. The front motor isn't separately speed controlled; it just rides on the voltage input determined from the tach reader on the rear flywheel. Hence, if it's not under load, it speeds up. The on-board electronics don't know how fast that front fly wheel is turning and do nothing to slow it when the work load on it decreases. The back motor does have the timing "tape" and reader and maintains its set speed even when you decrease the load on it by picking up the wheels. So one cannot infer from observing that behavior in PS2 or 3 engine that there is a problem.
I had a Dash 8 from the first (PS2) wide cab run with a bad tach reader. It didn't behave too badly, except in lash ups, when it was clear that it was running faster than its sisters and spinning its wheels and pushing against them. I sent it in under warranty and MTH changed the defective tach reader and had it back to me in about a week.
If you have a Z4000 or an amp gauge, you can see whether it's drawing unusually high amps, a sign of some drive train mechanical problem, such as binding. Otherwise, if the motors are indeed working, but the speed is off compared to other engines (i.e., you have to set it to 50SMPH to go what should be 30SMPH), you too may just have a bad tach reader. In any event, I agree with Barry, return it or send it in to be fixed under warranty.
RM