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Ford 4000 PTO quits

3-cylinder or 4-cylinder? Which transmission? Answering those questions will help us figure out what's wrong.
 

Yep! Way too skimpy on the info for us to have a ghost of a chance to help you out. As indicated there were two completely different 4000 models and each one had several different transmission/PTO configurations possible.
 
That PTO is controlled by hydraulics. When was the last time that you changed the hydraulic fluid in the rear axle? The fluid might just be old and getting thin when warmed up. If changing the fluid doesn't help then you may need to rebuild the pump. The pump in the right side of the rear axle center housing is actually two pumps in one. The front section is the main pump for the 3 point hydraulics, and the smaller rear section is the pump that provides the power for the PTO control valve. The rear section could be worn while the front section can still pump good so the 3 point would work fine but the PTO would have issues.
 
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