Ok trying to figure out why my top wont function. I checked my wires from the 5 speed swap and all are fine. What happens is when I press either UP or DOWN buttons for the top, only my quarter windows go down but nothing coming from the top motor. I looked at the FSM and all it said was to take out the TOP LOGIC RELAY or something. Its not really too big of an issue since I can always put it up or down by hand but its still a little inconvenient. Any insight would be nice.

Did you accidentally switch the bypass valve on the motor itself?

Also, check the top stack fuses (top 2 on the left in the fuse box)

Yeah, seems like either fuse/wiring to the motor or the motor went bad.

I checked those two 20 amp fuses. I would think you hear the motor even if the bypass is opened of closed. Im guessing the motor is bad but I figure I would try here first. Ill just take it out and save the 50 or 60 pounds or however heavy it is

I had the opposite problem - top goes down but quarter windows wouldn't go down at all. Found there's a connection under the console (between the seats) and if you route around it (easy, just unplug one place and plug into the other side) the top still works from the dash and you can put the windows up and down using the power switch in the console (although they still won't operate in conunction with the top). Worth looking at since it is a free and easy fix.

I was actually probing around today. I put a dmm on the plug on the motor and got no volts. Did you take a pic of what your talking about? Im having a hard time picturing it