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This reply is probably a little late since I just registered.
I have the service manual for the 3600 series MF and it says the Autotronic will disengage PTO (with flashing light) when hydraulic pressure drops below 17 bar (246 psi) causing the PTO clutch to slip excessively. It will also disengage if the implement is blocked causing clutch slippage. That being said, the Diff Lock, 4WD, and Hare/Tortoise range changing would not function correctly if hydraulic pressure was low.
With what you have described, my guess would be that the Autotronic box is faulty. The fact that you eliminated the speed sensor being the cause and no other problems exist with the tractor, it makes me think the box is malfunctioning.
I have a 1994 3690 that had Autotronic problems with the 4WD. Power was available to the Autotronic box from the switch (which removed power from the solenoid to engage 4WD), but nothing was coming out of the box to the 4WD soleniod to disengage the 4WD when 4WD switch was off. The Autotronic box is expensive, so I did a little rewiring job and was lucky enough to fix the 4WD and retain the Autotronic safety functions. In your case, you could bypass the Autotronic box, but unfortunately, you would lose the safety net the box provides for the PTO, which is progressive engagement and clutch operation. Serious damage could occur to the tractor without these safety features.
You might double check the PTO speed sensor is adjusted correctly (I can't find the procedure if it even exists), and if so, I would buy a new Autotronic box, or take it to a MF dealer where they should be able to hook up to the box and confirm that it is faulty. I hope this helps a little.
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