Take it to another Honda dealer!
No 1st gear on the countershaft is just a 55 tooth gear (replaceable gear) but it meshes with the 13 tooth gear that is machined into the mainshaft .. I was wondering what was wrong with the C1 gear that it was replaced , if mud/dirt was in between the meshing gears (1st gear) it would/could mark/wear the C1 gear but it would also do the same to the mainshaft gear .. I also see at least 1 thrust washer was changed ..
Also there are somewhere around 10 bearings in the crankcase it seems odd they were all ok when the same dirt is going thru them ...