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Here's the issue:

1997 Toyota Tercel, Auto, 4-cyl...nothing major..bone stock

Alternator starts going bonkers, car won't hold charge. Change alternator. Alternator still makes bearing whining noise and battery doesn't hold charge. Change battery. Alternator whining noise happens with new battery. Find splice in main ground which is tatooed to the tranny housing. Replace main ground. Start car, alternator still whining. Check fuse box, find 15amp ignition fuse is part way out. Push fuse in...start car and no alternator whine (all accessories on). WHOO HOO...not done! Once car is put into drive or reverse, alternator whine starts again, battery begins to lose charge (RPM has no effect). Once car is in Park (RPM has no effect), alternator whine stops and battery holds change.

Now the tranny is run mostly on hydraulics and mechanical parts...what gives when the tranny is engaged, the battery drains and alternator overloads and starts whining noise?? I'm totally confused by this.

A Chilton or Haynes manual is not available for this car, therefore, I don't have access to a wiring diagram which would really help me out here.

Any thoughts?  

Some late model vehicles use electricaly controlled tansmissions. The computer controls shifting of the tranmission. These have electric solenoids in the transmissions to control the how the fluid flows. You may have a short in this circuit. Check out the Transmission Section of this Board.  

The Altenator is not whining. Its the belt. Put a brand new belt on there and i garunteee it wont wine any more.