Engine shakes BADLY!!

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
Good thought fishy. I once had a vibration and could not pin point it. I had my drive shaft re-tubed and everything else checked out and then a friend told me to take off the fan belt and see what happens, low and be hold the vibration ceased. Come to find out my flex fan had flexed so much that it was pretty much flat. I put a new fan on and no further vibration....