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drain your tranny fluid and check for bits of metal. sounds like you could have issues with the M/T that you installed. was it used? how many miles were on it? did you change your clutch, pilot bushing or anything else that should be done when you have the trans off?
the input shaft bearings are very easy to damage in the sr/ka trannys. if the trans is hung wrong or hangs on the input shaft for ANY amount of time it can smoke the bearing. hope this helps you out.
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