Well, by the RAW, probably. If they don't have a type of bonus, they're unnamed bonuses, and thus stack. I don't recall seeing a type associated with any of the caster level bonuses I've seen, so I think they all stack.
If that bothers you, you could simply assign types to different sources. I'd say a template would give a racial bonus, and an ioun stone an enhancement bonus. I know I've had this conversation with a DM of mine before, and that's more or less what he decided. My question was in regard to the +4 CL from Practiced Spellcaster, and the +1 CL for casting [Evil] spells with the Evil domain.