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The Scotch Yoke pump has 4 pump cylinders. If one of them isn't carrying the ball, there is a noticeable pulsation as the lift arms come up. It's a lot like how your engine runs when you pull off a spark plug wire. I suspect you have a sticking valve in one of the pump chambers. Once the fluid warms up and thins out, the valve frees up and can seal properly. Changing the relief valve is unlikely to help. A soft relief valve spring tends to lead to a loss of lift capacity, but the lift still works smoothly (albeit weakly). You could probably fix the problem by dropping the pump and cleaning all the crud out of there. I'll bet you don't actually need a rebuild. You can take the valve assemblies off the pump chambers and clean them up. Just pay attention to the orientation of the many parts. A soak of the complete pump in diesel followed by spinning the pump by hand with the PTO shaft will probably do it without taking it apart. The N-series hydraulic lift will pulsate some, even when new, if the engine is running at low RPM. This is a fundamental difference between a PTO driven pump vs. a front mount pump.
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