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sounds like your clutch needs to be replaced, could be a pre-exsisting problem with your transmission if you bought it from someone else privately. people do not really take care of their transmissions, it may be due for a flush as well as a little tlc....if its grinding and clunking you may need to replace the whole thing. but first check out all the gears, solenoids, filters, and flush the tranny before taking your tracker apart.

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Q: 2000 Chevy Tracker with a manual transmission All in all the tranny seems good but shifting from 2nd to 3rd or down-shifting from 5th to 4th seems clunky. Can the clutch be adjusted to fix this How?
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