You are not on the best axle, but you already know that. The 14 bolt will be better suited for the 43" sticky.
Teeth missing from one area like that usually indicates deflection. I'm willing to bet you are not pre loading the housing enough. The reason I asked your process, is that will sometime tell me what you might be doing that could be changed.
A setup bearing is okay. I do not use them for carrier bearing in any case. They will usually give different readings from real deal pressed on bearings.
That being said. How hard is the carrier to remove from the housing? Is it a mo fo, like got ya sweatin' you might not get it out or just a simple pry bar pull and it's out?
In a buggy that is simply trail riding or boucin' I set back lash tight. Somewhere around .004 to .005. This type of rig will never build enough heat to damage anything. They simply do not run long enough each time.
An Ultra 4 car or other race rig is totally different on back lash, but carrier preload is always always tight.
Give me a little more info about how tight the carrier is going in and out.
Rocky