Digging back into how we deployed this:
Pro Tools is a pain in the ass.
Initially I did simple before and after snapshot and we ran into some issues. Until the program is launched as an admin, a non-admin (student in our case) user cannot create or open projects.
As a result, we took the before snapshot, installed Pro Tools, needed drivers and instruments, launched as an admin once, then took the after snapshot.
We did not think to install the iLok license extensions in our package (available from http://sw.ilok.com/macextsx.dmg), but that would be a nice addition to your package.
Lastly, since we are physically tying the USB iLok device to a computer, I am working on an EA to list the iLok serial in the inventory report (and trigger one that goes missing with a smart group).