We build adapters for installing electric motors into many vehicles so this is not much different.
The old tranny is fixed in a CNC milling machine and all the bolt holes and center of input shaft are entered into the machine.
Then the new tranny in fixed in the milling machine and the same process happens. Next a piece of aluminum plate goes
in (or one of our adapter castings) and whiz, whir out comes an adapter plate.
Well not quite that simple but not much thinking goes into them anymore.
In the past we would spend hours figuring our centers and the "magic" number which was the spacing between the old flywheel
and the difference with the new flywheel so the clutch would work and you didn't end up pre loading the end of the tranny input
shaft. You usually have to change the pilot bushing as well to fit the new input shaft.

BFN
Randy