Either of the above explanations could cause excessive vibration.
I will add that your engine/shaft alignment could be out and your cutlass bearing could need replacing as possible causes for vibration.
It seems to me that the transmission is the likely culprit though. There are discussions on how you adjust the A4's transmission over on the Moyer Marine Community forums: Moyer Marine Atomic 4 Community - Powered by vBulletin
Our A4 shifts fairly easily into forward gear with little variation in vibration or sound.