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You loaded your new transmission into the damaged clutch. There is a small chance the trans got damaged by the clutch. Did you forget a dowel pin? They love to stay in the bellhousing. Check your old one. If you put the trans in with a missing dowel pin, you'll have a vibration for sure. A way to tell if the vibration is trans/clutch/misalignment related is to see if it subsides when you push in the clutch. If it does, it's in the clutch/trans. If it doesn't, it's more engine/flywheel related.
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