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The conditioner bearings will rumble if bad........or have a popping sound. If the rollers start to touch, obviously you'll hear it, and see it. Best way to check these bearings is using a pry bar to try to see if they're moving. I've replaced them once in the almost 30yrs I've owned the machine. I personally don't see any problems in these bearings ruining the pitman pulley shaft, or its bearings. The rollers are driven directly by the motor, prior to the sickle, auger, or pickup reel.
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I'm starting at the bottom.
Last time I ran the machine, I wasn't paying attention, and hooked a panel fence while crossing the creek. I finally looked back, and saw it. Didn't see any immediate damage. I'm not sure, but I think I hooked it with the ball joint. I noticed no problems during the day, until I stopped to oil the chains. At this point, I noticed that the machine was banging. The sway arm bearing had worked loose. The castle nut hadn't moved........there was just increased clearance between the sheet metal, and the sway bar pin boss.
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Today was the first time I've looked at it in a couple of years. The pin seems to be in good order. The sway bar is still straight. BUT I'M ZONING IN ON THE SHEET METAL. ESPECIALLY THE LOWER PIECE. I'm seeing a possible depression where the boss contacts the sheet metal. My thinking is.......the ball joint snagged the fence, pulled the sway bar, and the sheet metal yielded. This radically changed the clearance between the two halves. This is where I'll look when I get around to removing the sway bar. It might just boil down to a heat job, or cut & replace the affected sheet metal.
The sickle operates without slapping, and was cutting fine. I will inspect the left side of the bed, and sickle end, when I get around to it.
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Anything affecting the drive will begin at the top ball joint. Barring a mondo problem with the pitman arm that comes off the flywheel. I see nothing that can relate to your problems anywhere else. I'm surprised that the pitman case bearing shaft had problems........the belt drive isolates it from shock. I'm sure you examined the flywheel, and it fits properly on the shaft.
As far as any other "chatter", it might be originating from the auger, or pickup reel. Again.....use a pry bar to see if the bearings are bad. Might check your clutches while you're at it. They can freeze up over time, and fail to work when you need them. Way back in ancient history, I used to cut Haygrazer with this machine. The auger clutch took a beating, but protected the system.
Actually, I'm not sure what "chatter" is. These are noisy machines when running without load.
If you're trashing that pitman/flywheel drive shaft...............there has to be a shock, or imbalance. That's all I can think of.
IIRC, it was either on this machine, or my 1010, that I had to trim the sickle end to keep it from interfering with the high arches at the sickle end. Hell........it's been a while since I looked at the sickle, and can't fully remember how the parts were arranged on the left end of the cutting bed. If you run into something suspicious, I can look at it at a later date to compare notes.