I think your on the right path. Your feeling first order engine harmonics. Have you started it with the belt off to eliminate the accessories? Look that flywheel/pressure plate over very well. Look for any weights that shouldn't be there. I don't think the crank pulleys have any weights on them. If you're up for the work, remove the belt, the trans, pressure plate and clutch disc. Fire it up and see if it still vibrates. If it does, you know it's internal. If it is, maybe it was rebuilt and had a couple pistons replaced with units of different weight. Be curious to see how this plays out.