The deepest the rout needs to be is so that the pickups can be are flush with the tops of the pickup rings. There's no point them going lower for if the strings are catching on the pickup rings, there's something very wrong with the neck angle. You'll probably find the pickups sit a couple of mm higher than the rings when everything is finally set up.

If you are making your own pickup rings, then it's important that you make them the right height, so I'd look at the dimensions of replacement ones you can get on-line as a guide. You'll need to incorporate a curve into the base of them to incorporate the arched top of the guitar, so you also don't want to make the neck ring (the thinnest of the two) too thin otherwise it will easily snap in the middle. But it shouldn't be any higher than the top of the adjacent fretboard.