Manual motor into an automatic

Okay, might be a dumb question, but, can I  put in
my 1995 manual motor into a 1996 automatic?  
Am I under the wrong impression that it is the
transmission that makes a difference?
I bought my 1995 SL2 in Feb.2000 with 50,000
miles, after we moved to MN. When my now ex-
husband went looking at cars, my only stipulation
was that it had to be a manual. (In case the starter
or battery was bad, I  could still get home).
Over the years, having had to replace different
things, here and there,such as cabin fan,
thermostat, side mirror (from idiot in parking lot,
have no idea how) motor mount, exhaust pipe,
muffler, brakes (16 yr old drove home from target
with E-brake on entire way. There was smoke
involved), belt pulley, battery (2), water pump (6
months ago), ect.
Anyway, December of 2015 while I was on my way
to the University of Kansas Hospital, emergency
cardiac unit, because my eldest daughter had
suddenly been admitted, the engine blew! There
was a big 4 inch hole right in front. I had no other
option, than to get a different engine in it, to get
home. Cost me about $2400! (somehow, they killed
the AC in doing it, though). So, to the point I ask,  3
days ago, January 1, 2018 a guy in a truck ran me
off the road, I went onto the left shoulder, back
onto the road, bounced off the right guard rail a
couple times, before coming to a stop, facing the
wrong way. It messed up my hood (some) front
bumper, bent the driver's door (only latches the first
one) bent the trunk lid, maybe, left wheel is kinda at
a little bit of an angle wheel-well drags on tire, but
completely shattered the left quarter panel. Most
of the gas cap is missing.
I know, long story.
So, can I take the engine that is in my 1995 manual,
and put it into an automatic that has a blown
engine?

Thanks! Michelle