I have the same configuration you are talking about, TTR 26r hubs.
Couple of observations:
1. Various versions of the castellated nuts (original, replacements) have different levels of cut. The newer ones can be shallow compared to where the holes in the shaft are. An easy fix is to simply deepen the cut in the castellated nut to allow the shaft hole to be fully exposed. Should not take much. But, your problem may possibly be the one below.
2. Ensure that you have the hubs installed correctly. The inner and outer bearings are installed differently on the TTR 26r hubs than on the stock hubs (or apparently other 26r hubs). TTR failed to supply me with instructions, so I initially had them installed incorrectly. It is the outer bearing that is inserted from the inside and
secured by a circlip - completely different from the stock hubs. If this isn't done properly the whole hub may not seat far enough in to allow the castellated shaft nut to be screwed down enough to fully expose the shaft holes. Also, the hub holes allowing the introduction of the cotter pin from the side will not line up either. This happened to me. As well as having the outer bearing shift during driving and loosening the hub. Fortunately, I got this corrected before much damage occurred. (I also found the OD of the original D washers was too big to fit inside the TTR 26r hubs. Initially had to grind the original ones down to be able to use them until TTR supplied some new ones that fit - smaller OD.)
Once I sorted out these issues things lined up: Hole in the hub, holes in the shaft, castellated nut groove.
Sorry for the out of focus shots, only ones I have of the situation:
BTW:
Two other points:
1. I used a dial indicator to set the end float. Precise. Never quite comfortable with other methods of tightening and then backing off.
2. I created an interference fit rubber disk to press into the end of the 26r hub to protect against dirt/moisture entering the outer bearing. There is no dust cap (that I am aware) for the 26r hubs.
HTH