It sound like to me that the snout on the spindle is out, can you check perpendicularity of the snout? As a side note I am working on getting FC hubs made since they are so hard to find.
This occurred to me, but I really don't have any good way to measure to that level of accuracy. Less than one 1/100th of an inch at the outside of a 13" brake rotor translates to a thousandth or less at the spindle.
With that said, I actually have made a lot of progress on this problem. I changed two things, and I'm genuinely not sure which did the trick, and frankly with it working well diagnosing what went right isn't a huge priority.
First, I revisited how I was installing the hubs. The FSM procedure is really weird and I started looking around for "unofficial" advice from experienced people who are running these types of hubs at high loads. What I found was that I was likely way over-tightening the bearings, Timken's advice to get it in the neighborhood was 50 ft-lb to seat, back all the way off, 10 ft-lb, then back the nut off a quarter turn. The way the FSM reads is you want to be able to hang a couple pounds off of the wheel stud without it moving, which requires cranking the bearing down way tighter than that.
The other thing I did was source blank brake rotor rings from Coleman racing, which I've anecdotally seen more than one person recommend. I have been running Z1 motorsports sprinkle slotted brake rotors with the Ronin Mandeville kit and it seems likely that Z1's quality control and metallurgy is not great. If I did it over I'd probably go to RacingBrake for my rotors.
I'm tempted to measure the current runout and maybe swap the Z1 rings back on, but like I said the brake feel is vastly improved and I'm mid-season so having the damn thing working is all I really care about right now.
FDF makes a kit that swaps the whole front suspension out, and their knuckle uses the bolt-on 350z wheel bearing. I really wish someone made a replacement knuckle that did the same thing but without the extreme drifting suspension and steering geometry.