Allisons come in a variety of configurations, even within a single model line.
Overdrive, direct, underdrive, retarder / non-retarder, one neutral position or two, pto / non-pto, etc. If you're putting this into a deuce, make sure you get a non-electronic Allison or you'll end up having to put an on-board computer in to control up and down-shifting, and kick-down.
The bell housings are SAE bolt pattern so bolt-up isn't a problem although you may need to go with an adapter, SAE3 to SAE2 if I remember correctly.
The question boils down to how much time and effort, and money do you want to spend on the project?
Allison has a whole bunch of information available to help you make some sense of it all. Also a little handbook called "Mechanic's Tips" that takes you through the installation and set-up.
These are free(?) from your local Allison dealer.
Once you've made your choice, you can always start scouting the local truck wrecking yards armed with a specific model/build number. The serial number decodes to how a particular transmission was built.
The litany here is "read the manual" and it's definately true with this one. Doing your homework can save you a lot of grief and headaches and wasted effort.