Welcome to the forum!
The models in the book come from numerous sources and I'll let Barry tackle that, but I bought some ECW clubmen from Warlord that fit in very well with Warfare...
http://us-store.warlordgames.com/search ... &q=Clubmen
The clothes may be a little anachronistic, but they work well enough for peasant mob types.
As far as weapons go, don't worry too much about exact ratios. You are correct that the entire unit should not be armed with muskets. If you mix in half muskets and half clubs that's fine too. Most of the equipment is meant as guidelines. For instance the army faction lists bayonets for musket armed troops. However, not all soldiers were equipped with bayonets in the early part of the period. If you model your collection on Huguenot foot of 1690 and you know they didn't have bayonets, you should not feel obligated to use them. In your example, the spirit of the cultist list is that they will not be armed as well as professional troops. As long as you use a mixture of weapons, your forces would be welcome at my game table.
As another example, the cultists have a Character we've called a ghoul. The Character is granted abilities that seem supernatural, but are based on the superstitious perceptions of the cultist opponent... Unless you prefer a more fictions setting for your game! The ghoul could be simply be a deranged psychopath with a cleaver, a sinister assassin cloaked to appear as a wraith, or a loon who thinks he's a werewolf... or if you like, the ghoul can be a REAL undead creature if it suits your game!
Most of the factions allow for a huge scope of customization and creativity and I am really looking forward to seeing where people take these rules!