a few things to check:
first, you said that the e-brake circuit is functioning. make SURE that the dash light comes on when you pull the e-brake.
second, when you undo the latch to the top, do the windows roll down a few inches, or do they stay all the way up?
third, since you have a '98, your switch at the top of the windshield actually is TWO switches. one of them rolls down the windows when you unlatch the top. the other completes the circuit to allow the top to deploy.
fourth, it could be the vehicle speed sensor circuit (makes sure the car is stationary before operating the top). see this page
http://www.iq.dynip.com/~gary/hacks/cabrio/cabrio.html for pictures of the relay and for which pin recieves the speed sensor signal.
if all of those things are fine, remove and test the motor.