Is the engine idling rough in park or when it's in drive and the car is stopped? If it's OK in neutral and park but shaking bad in drive, it's bad axles. The previous owner could have put in cheap axles with lots of play and vibration.
You should have just pulled the engine for this. Is the timing belt on correctly? Triple check that all the marks are correct. I would not quit and sell now after all this work.
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