The top operation probably quit because the controller did not detect that both windows were completely lowered. On a car built up to 12/93 this could be a faulty limit switch in the bottom of a door. From 1/94 on windows must be "synchronized", and to do this you close the window and continue holding the switch for a couple of seconds after the window is fully raised.

Regarding the use of the tool, from other posts carson356 is apparently willing and able to email owner's manuals. I would try contatcting him.