The clutch is connected to J4 on the main board. With the power off disconnect J4 from the board use a multi meter to check the clutch for the proper resistance which is between 10 and 28 ohms.
Leave the J4 connector disconnected power the game up the D54 led on the main board should remain off, If the LED turns on then the fault is the main board.
If the LED is remains off then check the resistance from each of the wires on the J4 connector to the earth ground on the power supply with the game powered down. If the reading is less than an ohm then the clutch wiring is shorted to the body of the clutch.