welcome aboard !!
you have loads of options . . . .
skil-saw
sawzall
jig saw
I often provide responses as if the issue were approached in MY world.
if it were MY boat, I would not go to the trouble of removing the wood portion
of the transom if it has a lot of caulk, bolts, etc etc.
Just mark the section to be removed and put a skil-saw to it.
I have NO problem with cutting thin aluminum sheet and plywood with my hand power tools.
BUT !!! This is a ONE TIME DEAL !! Ponder it in your mind if this what you want to do.
measure about a dozen times, mark with a black marker..... and cut it.
If you are not that experienced with a project like this, remove all the caulk and bolts.
Remove the wood transom - if it is in bad shape, now would be the time to make a new one.
Cut out the section that will make your motor work with your boat.
After you cut the transom, put it back in place. . . mark the metal hull.
cut the metal skin where you can FOLD IT OVER the fresh cut wood . . .
this will be easier done if it is bolted back into place as if it were to be permanent.
Take your time, MEASURE, MEASURE and MEASURE some more.
in the future if you get a long shaft motor again, just add a Jack Plate. That is simple also.
Enjoy !!