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Josh,
Welcome to the group, and particularly to the "black sheep squadron"--so named by another JD 400 owner for some of the unique features of this venerable tractor. Where is your hydro leak? I'm wondering if that leak is related to or the cause of the problem. For example, if there is a leak in the hydro fluid pick-up tube (big elbow tube coming from the transaxle reservoir to the tranny), the pump will pick up air causing foaming in the fluid and weak hydraulic function. Also, check to be sure one of the implement spools is not stuck at its limit. Work all three levers a bit and convince yourself all three are returning to center. A stuck spool will steal fluid from the power steering and other circuits, and affect transmission speed (although I have not seen a fully disabled transmission).
Harold
 
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Josh,
From the symptoms you describe and the checks you have done, it is logical to question a relief valve. There is no relief valve in the hydro pump--just a cone on the left side and a plug on the right side. The system relief valve (also described as a bypass valve) is located in the front of the implement valve body. You have seemingly checked this assembly to make sure it is clean and that the spring is intact. Charge pumps do wear out, but it makes no sense to have one fail suddenly. Do you have a hydraulic pressure gauge to measure pressure at the front quick connects? Does the on-board hydraulic cylinder work to lift the mower deck (if attached) or 3-point hitch? Does the power steering work? If you activate an implement lift valve or power steering with the hydro lever in the forward position, does the tractor move? Is there any chance that the driveshaft front key or engine flywheel key sheared and the drive system is slipping as any load demand is placed on the transmission? (You had presumably removed the driveshaft back end and key to check the charge pump pin, so there should be no issue there).
Harold
 
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