I just bought my 2006 Roush Stage 2. With only 20,800 Miles I knew the top was not working when I purchased it. The day I looked at the car I lowered the top with the switch it worked fine. Then absolutely nothing when I tried to raise it back up. I do not hear the relays in the fuse panel clicking when I press the switch up or down. I do hear a clicking in the drivers door when I press the up or down button and occasionally the passenger side window will go up when I press the top button then, it goes back down when I press the opposite button.Here is what I have done so far.
1.) Serviced the pump with ATF
2.) Swapped the relays (bought new ones and tried them too, nothing) they do NOT click
3.) I pulled relays and checked for power on the correct slot, I am getting power at the relays, but they do not click
4.) The 5 amp fuse in the passenger side panel was blown and I found corrosion on the entire panel, I removed all plugs and fuses, cleaned with QD Elec cleaner and brush to remove green and white corrosion. Applied di-electric grease to all connections and replaced the 5 amp fuse.
5.) Checked for power at the hydraulic pump/motor, I am not getting power when I press up/down button
6.) Applied 12v directly to the hydraulic pump/motor and nothing happens.

I am so confused by all of this. Power at the relays but no clicking when button pressed. Swapped with brand new relays and same thing, so I think relays are good.
No power at the plug for motor, and direct 12V to the red or yellow pin does not do anything.

 

Sounds like your problem is in the SBJ, especially since you found corrosion already. I would get a fsm with wiring diagrams. I have a convertible myself and can tell you that when you press the switch to lower the top, all windows will go down before the top does.