Thanks Jim. Under no circumstances should you ride or even start this bike again.
The fact that the gearshift functioned normally by hand but grinds when running
(under load) narrows it down to about a dozen possibilities.

When you rebuilt the bottom end, did you replace all the bearings? Did you check
the tolerances on the two shift fork shafts and the three shift forks? Did the bearing
on the shift drum spin freely by hand? Did you ensure all the thrust washers and
spacers were installed in the correct locations?
I know there are a lot of questions but it sounds like one of the shifting components
(shift drum, shift fork, shift shaft, etc) is binding under load possibly from loose
tolerance or a bad bearing or possibly a missing thrust washer. In any case, you will
need to split the cases again. The first thing I would do as you disassemble each
component is verify that every thrust washer, spacer and circlip is present and seated
per the expanded diagram. Then use a dial indicator to measure the shift forks, shift
fork shafts, and shift drum to make sure they are within spec. Also look for scuff marks
or rings on the shift fork shafts. This would indicate binding. It's also a good idea to
make sure all the bearings spin freely and are seated completely.
All it takes is a worn shift fork shaft. As you try to change gears the shift fork "cocks"
very slightly on the shaft and binds, refusing to move.
If you try to run this engine without correcting this problem, you will probably end up
with a case full of expensive metal pieces operating randomly. My advice is to park
the Honda for now and borrow a friends bike to race until the CZ is ready. This fix
could take some time.
dogger