I just thought I would give you a heads up I bought a hobby cutter 12" sticka by roland it has gotten a lot of use but as far as making the stencils you are needing it is limited not only by the 9.8 inches wide maximum but it will not cut any longer than 39.97 inches long. I thought I would be able to make a 4 foot stripe with it if i needed to but sadly it is not capable. I am a bit of a hacker as well so it isn't due to an inability to use the software or hardware the machine is simply not capable of doing it. I bought it on ebay 4 years ago for $450. I have figured out how to make 50 inch windshield strips but it won't make a solid stripe over 39.97".
As far as the file format illustrator & Corel Draw seem to be the norm. .eps .ai .cdr .pdf