I'm pretty sure when I did my first engine (340) and that engine shook tooI had a different 2500 stall converter, I switched to the new tci 3500 with no cure.
Are you using the same water pump and pulley's you had on the old engine? If so you may try taking all the belts and the bottom pulley off and firing it up and see if something there is causing it. I've seen bent water pump impellers cause a heck of a vibration even if their not bent bad