You cannot shift ANY motorcycle trans completely through all gears without the trans input shaft turning, it is what allows the gear dogs on sides to line up whereupon the gears then move into full engagement. Don't spin the shaft and you are intentionally bending the shift forks as it is impossible for the shift to complete until those side dogs line up. One shift or another will complete if the dogs line up just by luck but not nearly all shifts will work.
'It seems as if the pawls dont make contact with the drum pins.'
Well of course they don't; the shift drum is half out of time as it cannot go all the way into full gear engagement. Where you end up with the fork pinning gear to one side because the dogs don't line up. You don't get any feel from that condition at all. Thinking you can go from 1 to 6 without rotating any shaft should be impossible. You are saying all 6 sets of dogs are lined up to do so, somebody would have to split the cases to line up each gear by hand to do that.
I rebuild manual transmissions blindfolded, I used to set up Doug Nash full race 5 speeds for 10,000 rpm SBC and I rebuild automatics too.
I sense some BS here, I could be wrong but I can't see anybody working on a CBX with thinking like that. I note the other trick bikes mentioned too, a wish list if you ask me, the experience level posted here is clear enough.
I haven't done Honda SOHC (I have a CB550F but it refuses to break) or Z1 yet but they are just more engines to me as I have done hundreds of both car and bike, I raced Kaw 3s and Honda DOHC 4s. Plenty of 2 stroke but some earlier than RD, say YDS3-6B and YM1-2 250-305 and a bunch of them. That shifter was the shifter from hell as compared to RD stuff. Later full honk 10,000 rpm S3 400 Kaw triples I ported, restoring an H2C 750 right now.
If I'm wrong about you then I apologize but you still have to prove it to me yet.
Start turning the input shaft the clutch attaches to and THEN shift trans while doing it, the faster you turn it the better it works. The trans should be able to shift through everything with little trouble. You have to do that on bike trans as there are no true synchronizer rings in them like cars have. The side dog on the gear is the braking method there.