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The next time you pull the trans you might check the second third sliding gear on the main shaft, you said it was jumping out of gear. Ford recommended changing that if the main shaft needed replace, many people concluded Henry was trying to sell parts. You can check that by grabbing the gear when the tower is off and try to move the gear by a wobble on the shaft. The amount of clearance necessary should be only enough so that the gear slides slowly on the shaft with oil in a vertical position. Been there done that, and it’s not always the easy fix by tightening the spring and plungers in the shift tower. Bearings on your main shaft will swap oil and or grease if those bearings don’t have seals in them. Leaking from the trans to the front of the bell housing, can be eliminated with a real deal transmission seal from Mitchell.