The inner adjusting nut position has nothing to do with the outer locking nut coming loose. Not unless the pin is missing.
As far as the pin aligning with the holes perfectly at 90 degrees, you just got lucky that's all. There is usually some fishing involved no matter what. But sometimes you get lucky and it just falls into place. So no foul with having to do it at 45, but I would still double check the end play as it might be too tight.
What you did by only backing off 45 instead of 90 is potentially change the final bearing adjustment. Backing off 90 degrees is specified and they knew full well that doing that leaves you with excess bearing play. But only temporarily.
What gets rid of the play is the 100lbs of torque you put on the outer lock nut.
If you have it apart again (and personally I would do it, but it's up to you) do it per spec to the 90 degree mark, check free play and then torque to 100lbs and check free play again. it should all be gone but about .005" or so.
Something is either wrong with your hardware, or the threads on the spindle, or something else is going on. Do you use it hard (like it's supposed to be sort of)? Or is it a street rig like most Broncos? If a street or gentle trail rig these things should never come loose. Most will run 40,000 miles and never come loose.
I can't claim to have checked that theory, since I used to re-pack and re-adjust mine about every 25 to 30 thousand or so. Never had the chance to check it at 40k, but they were not even remotely loose at 30k either.
I wonder if you have a set that is machined out of true? If the two nuts were not sitting square on the threads, or the mating surfaces where the locking ring rides on them is not flat, then they might come loose like you're experiencing. Same for the locking ring not being perfectly square.
Anyway, if you feel confident there is still enough free play in your bearings with the 45° back-off, you should be good. If not, you should re-do it. Again...%) Ugh. Hate doing things over, but sometimes you need to.
If it comes loose again, try using 120lbs of torque the next time.
Paul