Rule #1 CRs are an art not a science. The numbers do not always make fair CRs. Look at what the PC party can accomplish, and use that to assign the CR once the HD increases have gotton you to the ballpark number.
Creature Type CR Increase
Aberration, construct, elemental, fey, giant, humanoid, ooze, plant, undead, or vermin +1 per 4 HD added
Animal, magical beast, monstrous humanoid +1 per 3 HD added
Dragon, outsider +1 per 2 HD added
BTW Feats listed in monster entry are only typical, not racial unless listed as such. Some might feel designers intentionaly "threw away" feats on "alertness" and "toughness" to keep creatures at lower CRs, others might feel since the Players have access to more potent feats from splatbooks, the monsters should also be using those splat book feats.