Engine Swapping from an Auto to a Manual Transmission

I own a 95 Mitsubishi 3000gt. Base model. It's an
automatic. Im looking to buy a parts car which is a
98 Mitsubishi 3000gt. This is a manual
transmission. The parts car has a motor that
knocks and blah blah blah everything else is good.
My motor runs flawlessly. I was wondering if it was
possible to swap my engine coming from an auto
straight out of the factory to this manual version.
The way the engines and transmissions are
designed, are they compatible to be exchanged?
Reason for asking. I love my 3000gt, but I would
love it more if it was a manual. Besides. My auto
tranny doesn't seem like it will last much longer.