The 5th gen civic's with the gsr swap need a slightly different drive-shaft, so that would be the likely issue IF the teeth would solid. That piece (98% positive) should be stationary, not loose. Check with your local Honda/Acura mechanic, and get some solid advice. Anyone with knowledge enough to have a 5th gen civic w/ GSR would obviously know that alignment needs attention and would know what that feels like. Plus, unless you had a B series motor, which most 5th gens don't, you already replaced the motor mounts in the process, which would be more constant with the trouble they cause...

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Good luck,
MiniMe