When replacing parts in a manual gearbox, do mating parts need to be changed together?

I’m trying to diagnose a notchy/difficult shifting condition for a 1-2 and 2-3 shift. This is a M5R1 / M5OD (Toyo/Kogyo) transmission that was recently rebuilt (by me). Vehicle is a 1998 Ford Explorer.

The slider/hubs had a lot of wear on the teeth, so I replaced the 1-2 and 3-4 slider/hubs with new ones. I did not replace any of the gears that mate with the slider/hubs.

Now I am wondering if these parts need to "break in" together, if they will ever break in, or if I have some other issue. The gearbox has had about 500-1000 miles on it since the rebuild and it hasn’t changed much in that time.

The synchros were all replaced as part of the rebuild.

Any suggestions would be appreciated before I decide to swap the whole box out, or try tearing it down again.

Edit: Using an endoscope through the fill plug, I took some pictures of the hub/slider/gear assembly for 2nd gear. The drained oil had some fine gray particles in it but no chips or anything sharp.