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Turns out the problem in the primary was not a bad compensator. I bought the bike used a number of years ago and am still learning what modifications have been done. Apparently, the prior owner put a HD automatic chain tensioner in for the primary chain. When my indy pulled the cover we found that there was no slack in the primary chain and this was causing the hard shifting and loud clunks when shifting. Luckily the inspection of the spline on transmission shaft and clutch are ok and the bearing on the shaft turns smoothly. Will still need to inspect the bearing. From what I have been told this is a common problem with the HD Chain tensioner. My take away is if you have a HD auto chain tensioner take it off, if you're thinking about buying one, don't.
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