Engine/Transmission (1994 - 1998) 95 and 97 engine differences when hooked to auto vs: manual transmission

[SStryker]

What are the differences in engine components in a 1995 dodge 3500 cummins engine thats hooked up to an auto vs: one hooked up to a manual transmission? Horsepower is lower for auto. Same question for a 1997? If we wanted to put one of these engines, either the 95 or the 97 in both cases that are presently in automatics in a different truck and increase horsepower to over 300 which one is the best engine and why or doesn't it make any difference? Thanks