You've now verified that everything is correct. I don't believe that there's even a possibility of getting the wrong kickstart shaft; and, the odds that the thrust face was incorrectly machined are lower than picking the winning lottery number.
We've all been going on the incorrect assumption (and getting by just fine) that the pinion gear teeth makes 100% contact, same as the C/S & mainshaft gears do. Yes, assumption is the mother of all
ups. That said, even in this ultra-harsh light, there's a very logical reason why I'd not criticize anyone over this issue, namely..."
if it ain't broke...". Realistically speaking, this breakage is uncommon, if not rare; there are only two major parts involved (3 if you include the C/S gear) and they're completely taken for granted, except at rebuild time. So, anyone going through an engine where the shaft & gears are still in tip-top shape would naturally assume that nothing would be affected by simple R&R...because of a highly successful track record.
Just an FYI, the only setup known for kickstart gear-related breakage is the older Takegawa 5-speed, when used with their old 124 superhead tune. Stuffing more gear pairs inside those case requires thinner gears. The OEM Honda 4-speed gears are significantly wider and stronger...which is why I sometimes refer to the 3-speed as the small Honda equivalent of the Powerglide.
Okay, back on topic...
There's still the money question to be answered..."what caused the failure in the first place?". Apparently, it wasn't a part(s) or assembly issue. It strikes me that you're now back to square one, but with new parts. If everything is the same as it was, what's to prevent a repeat performance? I'm not playing devil's advocate here. Hardened gears don't crack, they chip & break; they're brittle. It's possible that one tooth was partially broken & you missed it; no way to ever know if that's what happened at this stage. The short story, in an already long post, is that starting technique is virtually the only place left to look.