well, after some time and around 500 kms there's something to share.

bike is rideable - that's best thing to start with.
clutch was re-assembled in proper order.
also, this time paid more attention on alignment of gears of axle and push rod (these xts' have clutch shift mechanism on the right side). the result is perpendicularity of clutch cable and pull lever (while clutch is being engaged), thus giving the best leverage.
and suddenly clutch gets much softer.
and, more importantly, i could select the gears normally!

from the beginning, clutch used to get slippery, then i had to feed down the cable. some more time, again slippery, bit more adjustment... it happened several times, with quickly decreasing rate.
the reason seems to be some groovy wear on pressure and some friction plates: after re-arrangement this grooves met with flat surface, resulting much less area of contact to wear first and quick.
anyways, already got new clutch kit, now waiting for pressure plate to arrive.

since the assembly, gearbox downshifted from 5th to 4th only once, and one false neutral has happened.
only remaining (or transformed) problem is that now it's neutral to find hard, but it reminds about itself mostly during longer red traffic lights only.

thus, for now the issue is not completely solved, although, it's no more big issue at least.
really didn't expected that proper order of clutch plates could make such essential difference (considering that new oil and better alignment of axle gears are secondary factors).
the time will tell how it will be after new clutch and pressure plate, as well as proper cable adjustments after break-in...

cheers!

Its something strange, mine is perfect some days and others a mess. Seems like problems is worst when you do a emergency stop in high gear, i need to drop clutch a little to get it to gear down. On normal riding its never a problem, hard to tell whats out of sync.

well, so far there're just couple things in which i've became certain - be it shifting problems or clutch slipping, it was less likely to happen on colder engine in my case. also, proper order of clutch plates, alignment of push rod & lever, and cable adjustment all make big difference how gearbox behaves.

stopping in high gears was also bit tricky for me as well - even before problems mentioned in the first post, gearbox sometimes not completely followed series of quick downshifting inputs. for now, after re-assembling the clutch, don't remember if i had to do this so far.

Have been testing today, its impossible to gear down if bike is in 3/4 & 5th and i stop, have to release clutch a little and doesnt matter where wire is. No problem when rolling bike, you can tell huge difference on how amooth it gears if you find sweet spot on wire. 2 gear is possible to shift down but it want to stay in neutral, never had this problem on 3tb engine, seems like i have to make one engine of these two.

rolling the bike a bit or releasing the clutch a bit - guess both mean some rotating input into gearbox from different sides. and yes, in some particular cases without such input selector drum is unable to switch. i used to think that i understand basic operation of my gearbox, but seemingly my knowledge is not enough to explain such deviations.

Its because they are not in sync standing still, thats normal but its a little bit to much distance i think. Thinking maybe they are not sliding as they should.

https://youtu.be/g8xnIFf4id4

https://youtu.be/h9MkzOkaHd4

yes, such animations used to be pretty helpful for understanding normal working order.
which, on it's side, could benefit to understand when something's abnormal.

to put simply, there could be some other issues caused by wear.
turboguzzi mentioned about bent shift shaft.
your clue about not sliding well also makes sense. input and/or output shafts could also be bent.
according to current practice, there's pretty big chance that i'll be able to keep riding (considering replacing clutch and pressure plate). then time will tell about further needs like splitting the case and need of other parts.