I have a 95 5 speed and need a new motor.
I can get a new 1995 automatic drivetrain (Motor&tranny) for a good price. Is this going to be a drop in or will it need alot of modification?

You should be able to use the motor regardless of what type of transmission it was hook up to. I'd keep the same type of transmission though. Not only do you have to swap the transmission, but you'll also have to get wiring, cables, interior trim, as well as possibly a new computer.

My 2 cents, i think the automatic and the stick; the main difference is the idel. the auto is approx 800 and the stick is 900.