Sorry to hear no joy. The limit switch for the tonneau cover can be accessed without any disassembly. If you have the wrench to unlock the cover from behind the rear seat, raise the top manually. You then need to raise the bow (rear) of the top and then lift the cover. You'll see the limit switch on the driver's side, the lining for the soft top compartment is held in by plastic rivets.

The other limit switches can be inspected once you remove the side interior panels, not hard or time consuming. Once the seat bottom and back are out the panels just screw in and one hex screw at the rear. That would allow you to inspect the connections. If you lost both seat belt presenters something may have come apart. From what I could see the presenters have separate relays. You may want to do that before swapping out the controller.

The fact that your CST switch is always lit is another issue, usually that means it is available to operate the top but not here.

Something is telling the controller that all systems are not "go" it must think the roll bar is not fully retracted or the windows are not down. Is the roll bar inop using the dash switch? If you can raise and lower it I would cycle it a couple of times.

If you manually raise the top is it also not responding to the switch if you try and close it? From what you posted before about tricking it into finishing the lowering cycle your CST controller is doing something.