well, I WOULD think that any movie-maker program will do it fine, I even think that windows movie maker is good for it!
regarding the song, what are you looking at doing? For example, the stop motion would be AAAAAAAAAAAAWSOME if you did it epicly just plain drawings to perhaps Amon Amarth "Embrace oif the endless ocean" or an equally epic power metal song, where the story is really strong (also Blind GUardian "Sacred" for example) but the rythm isn't that fast, since both songs are kindof long so that it wouldn't be so many pics!
I'd love to help you, (hell, I'd love to do it myself!) but since the army takes much time, I don't know if I can. But just poke me in game or send me an email (dahl102pluton@gmail.com) with the questions or whatever you wanted help with and ill try and answer them! The mail is sure to reach me, since I check that almost every hour
Good luck with it greggboi! and I look foreward to see it!