David,
You can, of course, set the individual pin out's for the DB25 within Mach3. In addition I think you will find that the Theta control (tangential steering) is handled better by Mach3 but I have never done an exact comparison with EMC2.
Please let us know how you get on with EMC2 and which CAD programs you use to create the tool-paths for your vinyl signage.
Good fortune with your project.
Tweakie.