A couple of things I would check:
You have already verified there is no parasitic draw.
Is your alternator properly grounded? Take a 10 gauge wire from your alternator case to your negative terminal. You cannot always count on the bracket to ground it.
What kind of shape are your battery cables and alternator wires in? Corroded ground cables will limit the voltage you see even with more grounds installed between the body and engine. A quick and dirty check is to measure voltage (with the car running) between the alternator stud and at the battery post. If they are more that 0.2 volts off you probably have a cable issue.