Have you tried Expect? It is used to control external applications, and is good for scripted response flows.

But based on past experience, I'd strongly suggest modifying the application to have some sort of "batch mode" where it just does what it is told and doesn't try to interact, and then just call that. This will make your life a *lot* easier. And in the long run will be less fragile than trying to script what to do for every unknown prompt.