or did the clutch just lock it up? At this point the latter is the situation for me, but it started out intermittent and the pilot would work sometimes.

I've been assuming the rudder reference has been working -- but I'm going to do the following test I found on the Raymarine Community Support site. The article is titled "Drive Stopped or MOT STALL message on autopilot display":

"Drive Stopped" or "MOT STALLED" is a message from the autopilot's course computer indicating that it is not able to turn the vessel's rudder. This is a broad error message indicating that there could be a issue with either the steering, your Drive unit, the Rudder Reference Unit (if fitted) or the Course Computer. To figure out what item is causing this issue there are a few tests that you can do yourself as outlined below.

Excessive Steering System Load

The rudder could be extremely difficult to turn due to a mechanical problem (jammed pulleys, cables, quadrant etc.), or excessive weather load (wave forces and sea action). These are both rare occurrences. Proper maintenance of the steering system would normally prevent binding or lockup of the steering gear. If weather load is the issue, altering course, reducing sail, or reducing speed to lessen the wave pressure on the rudder are the best solutions.

This could also appear if the incorrect Autopilot has been fitted to the boat. If the drive unit and/or Course computer does not have the required output to move your vessel then you could see this error. I would advise checking with the installer or with Raymarine.

Checking the Drive unit

If the drive unit has seized or the motor has failed then the Drive unit could be the cause of the error. To test whether it is the Drive unit that is the cause, with the all the wires (Clutch and Motor wires) removed from the Course computer:
•Apply 12v only to the Clutch terminals
•Then place another connection on a direct 12v (or 24v depending on the drive) to the motor wires
•You should see the drive unit drive. Leave this for a minute to test
•Swap the wires over the termianls so you reverse the polarity
•You should now see it drive the other way. Again leave it to test.

One note is that Excessive wear of the electric motor brushes in the autopilot drive unit's motor is the most common cause of this message. When the brushes lose contact with the motor's armature, the motor develops a "dead spot" and will not turn when electricity is applied to it. A temporary fix to the problem is to rap gently but solidly on the chrome ring that surrounds the drive unit with a mallet. This jolt will cause the brushes to move just slightly, and will usually restart the motor. This is only a temporary fix however, and at your earliest convenience, the drive unit should be examined by your Local Raymarine authorized servicing dealer, or the Raymarine Factory Service Center.

Checking the Course Computer

It may be that the course computer is not outputting enough or any voltage out of the Motor terminals. To see if the course computer is the cause. if you remove the motor connections out of the course computer:
•and place a Multimeter in the wires place and then press Auto and then make a +30 course change
•You should see voltage increase
•Make a -30 course change and again you should see a change in the voltage but the polarity would be reversed

Also place your Multimeter on the clutch terminals and check that there is a 12v output when in Auto.

Checking the Rudder Reference Unit

The rudder reference transducer is the device that measures the travel of the rudder. The course computer watches the rudder reference transducer to see that the drive system is actually turning the rudder. Running the rudder reference transducer beyond the range of the pilot's electronic or boat's mechanical rudder stops, or a total failure of the rudder reference transducer will prevent the computer from seeing any rudder motion. If it sees no change in rudder angle after commanding the drive to turn, it assumes the drive is not responding to commands. To test the Rudder reference do the following:
1.Looking at your display watch the rudder bar indicator and move the rudder. Does it move as it should?
2.Does the rudder indicator wobble/move not as it should? If it does it indicates that the rudder reference unit is malfunctioning.
3.Disconnect from the course computer and then Using a Multimeter check the following,
◦Cable colour ---- Arm position ----- Resistance
◦Green/Red ---- Any position ----- 5k ohm +/- 5%
◦Blue/Green ----- Anti clockwise stop ---- 1.66k ohm +/- 10%
◦Blue/Green ---- Clockwise stop ----- 3.3k ohm +/- 10%

Should a test fail then that unit will need to be looked at by a Raymarine service agent. Please make sure that you carry out all the above checks.