Now that I've (mostly) statted up my army, I've got a couple more fine point clarifications:
1. Gear for monsters: It's clear that leveled characters are built with CR that explicitly contains a certain amount of equipment. Do monstrous troops without class levels get any equipment as part of their CR? If so, how much? And if not, what about the listed equipment that all monsters of that type carry (e.g. a Balor's Vorpal Sword, a Solar's Slaying Arrows Bow, or even a Yuan-Ti's masterwork armor and weapons)? I would assume that the listed CRs would factor in carried treasure, which intelligent monsters will use (thus it is modifies the encounter level). Would there be any difference if a monster was given levels in a class on top of its HD?
2. Ability scores for monsters: Characters with PC or NPC classes get either the 25 or 15 point array for their ability scores. What monstrous troops qualify for the 25 point array? And is it permissible to redistribute the default 15 point arrays that are given to the monsters if the 25 point array isn't used?
3. Feat/Skill selection for monsters: Can non-bonus feats be reselected (i.e. swap an Ogre's Toughness and Weapon Focus for Power Attack and Cleave)? Can skill points be reassigned (per the MM rules on class and cross-class skills)?
4. Summoning magic: Sort of related to the Warhorse CR ruling. If a magic item is purchased that can summon monsters (e.g. Bag of Tricks), should just the gold cost be paid, or is a CR judgment in order?
5. Unbalanced magic items: Since class and equipment are factored separately, what's to stop an army from being a bunch of level 1 characters with 11 levels (0.8 + 2.2 = 3 CR) of gear buying terribly unbalanced magic items with their 133,100 gp worth of gear? Especially when they could buy powerful summoning magic, and get things like huge elementals? Given the baseline unit costs, it's possible to have 40 level 1 Wizards with nearly a million gp apiece.