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1) I've owned my 93 F250 (351, zf 5speed, 210k miles) for about one year. There has always been some chatter when the truck idles in neutral with no clutch pedal depressed. When you push the clutch pedal, the noise goes away. I'be been told this is mostly likely a worn throw-out bearing. Does this sound right?
2) I recently towed approx 6K pounds about 800 miles. Since then I have a wobble (bobble) in 3rd gear. It almost feels like the motor is missing, but it is definitely a vibration coming from the tranny. I have felt it occasionally in 2nd and 4th, but the majority of time I feel it in 3rd. Usually higher in the rpm range. I have no idea what to look for. Any educated guesses?
I would suspect you need a tranny rebuild. The throw out bearing should make more noise when you press the clutch in. On the other hand the ZF is known to be a bit noisy but I still say you need a rebuild. Bad bearing?
I've had throwout bearings that chirped with the clutch out and the noise went away with the clutch pushed in. I think there is something going on in the tranny. At 210,000 you may have some parts wearing out. Try draining the fluid and see what comes out. I guess you could also pull one of the pto covers and take a look inside. There should not be bits and pieces of metal/metal shavings laying in the bottom of the trans. Shafts should not be wobbly. Speaking from experience, if something is bad it's better to fix the trans sooner rather than later.
That is my best advice; mostly because the ZFs don't have them. There is a PTO cover on each side that can come off cleanlyish after you have drained it.