From what I can tell, the Alnico II magnets will give a slightly 'softer' sound, a bit more mellow if you like. To the best of my knowledge, there is no difference in output, other than the obvious slight differences between sets inherent in hand-wound pickups.
I went for Alnico IV in mine, because I wanted them for blues and classic rock. In all honesty, whichever you go for, I doubt you'll be disappointed - the Mules are some of the most discussed pickups here, and I can't recall seeing a post where anyone wasn't happy with the tone (doesn't mean there aren't any, but I haven't read them all!).
Hope that helps a bit.