Yep, just a fraction of a turn on either shaft would let dogs go in. Imagine three dogs & three slots slightly off line & need lining up. One full shaft turn would give you three times they line up. Sorry if that reads confusing.

imgur.com/a/wrI8uQM

had another go at aligning the lever shift on the shift shaft as suggested earlier and still getting odd gear selection felt like it was trying to pull away in 3rd
pulled the clutch cover again and found the shift shaft assembly had rotated the shift cam to what i presume tobe the highest gear where the pin is not on the outer drum and it wouldnt shift back down, got the clutch basket off and it now seems to be selecting again (sorry about poor video) if you do check you can see with occasional turn of the shaft it will appear to select all gears up and down? i may have to concede defet on this one and take it to a mech but would love to see the process through to end and on a positive it ran great idles well and revs out nicely

It your video it does not appear you are shifting all the way up and down.  Hard to tell.  They do not shift well on the bench which has been mentioned many times.  What I see is normal in that respect. 

Shifting is sequential, so if you are getting all 5 gears, it almost certainly must be assembled correctly. There is no easy way (or probably any possible way) to have third be first or something like that.   Try counting as you shift. 

There are several ways to verify you are in first gear.  Keep downshifting while rotating trans.  When you think you are in first, do the half click up to find neutral.  Neutral light should be on.  If not, you can remove the neutral switch and look for the protrusion that contacts the switch.  It will be lined up with the hole in the case the switch screws into when in neutral. 

Alternatively, remove the detent ball and spring and look for the depression the ball falls into when in neutral.  It lines up with the hole in the case the detent ball and spring came out of when in neutral. 

If you can't see down in the holes, you can feel for the switch "bump" and/or the depression with a long small screwdriver.or small stick.  The next click down on the shift lever is first.  From there you should be able to rotate the trans and observe the shift drum upshifting four more times.

Here's a pic showing the "bump" on the left that contact the neutral switch in neutral and the "divot" on the right the detent ball drops into in neutral.  Both are lined up with their respective holes when in neutral if your dash light isn't working. 

thanks again was finding neutral ok just felt like it was pulling away in a higher gear. stalled a couple of times and then wouldnt shift down, this could be just my mind playing tricks on me however
wonder now if this could be clutch related ?
it was selecting ok on bench which is why i moved onto reassembly
its selecting fine now again it seems
i will go back over the previous suggestions and check its all ligned up on the lever and selector
drop the clutch back in and try again
after that i will concede defeat and get a mech to go over it all before reassembly
cheers
D

When you say "it was finding neutral ok" and that means you had the light working in the gauges, then it probably was your imagination.

I helped a friend once that was convinced for a couple of weeks that they somehow put the trans in wrong because "first" was a higher gear.  Like I said, virtually impossible.  In his case he was finding a "false neutral" between second and third.  We confirmed it was not in neutral, got the bike shifted all the way down into first and everything was fine.

thanks,
i dont think its false neutrals..
more it feels like its pulling away in wrong gear
i could then get another gear sometimes two above that then it must have got to to highest gear as the cam was rotated over to the missing dowel pin location (which i presume to be top gear)
it then wouldnt shift back down untli the clutch was removed then it wanted to again
now clutch is off and can see the cam rolling confirm 2nd gear on that more easily am going to check the other side is lined up correctly with the splines in 2nd but hopefully as you say  i am thinking second is 1str and theres a false neutral between the two
also check the cam selector is lined up properly on the roller as per the supplied manual pages earlier in the thread i dont think its an issue beyond the mechanics of these parts, i dont think the trans can really be put in that wrong (although if its remotely possible i am sure i could achieve it)

imgur.com/a/Pjzg66G

ok have run through the gears again and checked the alignement of the selector in the stator side as pictured..

seems to be right?
thats in second gear

its selecting all the gears on the bench 1 down neutral and 4 up (with some fettling with the drive to get dogs to locate properly)
a bit worrying havent found anything obviuos but will put it back together at the weekend and see if gears are any better at selecting
cheers again

Looks a tiny bit off but picture isn't taken straight on and camera angles can deceive.  I'd guess it's close enough as long as linkage isn't hitting the case on upshift.

When shifting on the bench don't get tricked by the neutral pump half movement & count 'that' as 'a' gear. That sounds stupid now i've said it but!!.
I did see the mainshaft move within its slight end pay in the video but only because dogs were pushing trying to find fourth gear & coming up end on until shaft revolved a little.
I was confusing myself thinking its all back to front in the video until i remembered it's all reversed to one down 4 up in that terrible linkage box on the left.

i think i have all the gears locating and the linkage in line enough for it to shift up and down without restriction
i wonder if i am getting clutch slip rather than anything else possibly related to the clutch adjustment eccentric screw?
i will try it back together tomorrow and go from there
not sure i can face pulling it all apart again, not for a while after that though