Look for a Clutch Safety Switch somewhere in the clutch linkage, maybe under the footboard.
Also I think some M-F's had a safety lockout switch that requires the the transmisiion ho/lo range shifter to be at Neutral before power can go from the key to the starter solenoid.
That rubber cap looks like it is related to this. Maybe something broke off so now all you see is dead-end wires.
Will the tractor crank if you apply 12 volts directly to the starter solenoid control terminal? (make sure the tractor is in Neutral and zero throttle!)