With the newer automatics they interface with the electronic engine controls, might not be as easy to mix and match as in the old days.
The Allison's although electronic can be run behind a mechanical engine with not much more than a TPS and the factory Allison computer with the appropriate tune. This was done factory in RV's and other applications with mechanical engines before everything soon became electronic.
I'd hope it's possible either factory or with aftermarket controller/tune for any other new automatic to play nice with any engine other than what it came on, it'd be nice but don't count on it. Similarly I don't know what the Cummins repower engines are capable of talking with and running as far as transmissions (and/or what you can get tech support to help accomplish).
If you get started down the Allison path and need help with the controller part I can point you to a shop in PA who has had great success with them behind various mechanical engine repowers and even some interfaced with some unexpected electronic engine controls, mostly all in pickup trucks.
