Transmission Confusion
 

Just had a new 618 put in my 91 this last week and everything shifts perfect. My engine now feels and sounds completely different, can hear so much more vibration in the cab and even starting and shutting off feels different if that makes any sense.. Started it this morning and it sounded like a train chugging. Did this for about 7 seconds then idled fine and clear. Was wondering if and how could a transmission could play a part in this? Figured I'd get some opinions before taking my diesel to a transmission shop and them say there is no way they could of affected my engine..