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Hi Cheezit, thanks for your input. I pulled the starter this weekend and the bendix looked great. I put some power to the starter to hear it spin by itself and it sounded good except for some bearing noise when it spun down. I tore it apart and replaced the middle two bearings which both had some play in them, both 6203 bearings. Reassembled, the bearing noise was gone, reinstalled, and the knocking sound remains. Judging by the frequency of the knock, it sounds like it is occurring once per revolution. I very closely looked at the ring gear and as much of the flexplate I could see with a mirror and flashlight and could not see any cracks or other issues.
Since the sound does not occur when it's running, in fact the engine sounds great, it must be starter related I would think. Its just so odd that there was no noise beforehand, not it starts up as soon as I reassemble. I have tried fudging the starter all the way in and out to change the gear mesh, and I did notice the knock would change when I did that, sometimes it would skip a revolution or two and not knock every time.
I think my next move is to get a salvage yard starter for $60 and see if swapping it out makes a difference. Really not wanting to separate the trans if I don't have to.
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