IH mentions there are separate rules for creating skull-sevitors and cherubim. I see rules for making the skulls, but they show cherubim later in book and no rules for them.

Letrii said:

I remember a vague passage somewhere stating that the Cherubim are grown in vats, like clones.

I guess that a PC must have access to one of these hideous nurseries in order to begin crafting his or her own monstrosities.

The rules appear in the inquisitor's equipment section of the Inquisitor's Handbook.

You could also use the rules for creating cyber familiars when you are trying to customize cherubim.

I doubt that characters would be able to create cherubim on their own, such knowledge would probably be far beyond all but the techpriests specializing in such areas.

By rules are you referring to the fluff and stat block they have? I'm talking about rules for their creation like they have for skulls or can they not be modified in the same manner?

I got the impression that the creation of Cherubim is prohibited and not meant for players to take part in. I'd kind of compare them to unseen servants in DnD despite the obvious visual element. As a GM you can just use the core stat block, pick a task or two that each one is meant to complete and you're set. They are pretty much pure fluff as far as game impact goes.