That mainshaft is a zombie defense weapon of epic (OK, probably mediocre at best) proportions.
They don’t line up.
Back everything out and give it all some contemplation:
After making double-sure that the bearings were all properly seated and whatnot, the shafts line up a little better:
Install the shift arm shaft hardware:
Splash on some Hondabond and crank it all down:
At this point I think there’s a fairly large chance that the whole operation is doomed to failure. I don’t have the tools or experience necessary to be certain that the rebuild was carried out in an effective manner, and I simply chose to ignore many of the tolerance and spec checks listed in the service manual (because what would I do if they failed? I can’t afford any more parts). I think that’s OK though, just getting some hands on experience with the guts of this thing, and really coming to appreciate and somewhat understand how a manual transmission works is worth it. If this thing blows up then I’ll have to start saving up to get a professionally rebuild replacement c’est la vie.