Mt gear crunch, lots of trial.

[kivig]

Hi,
2008 1.3, 140kkm/100kmi. Symptoms I'm sure many have heard here about, but "the hope dies last" :)
When the car is moving all gears (5th to a lesser degree) show some random resistance and notchiness engaging, and the 2nd randomly grinds teeth.
Much worse when cold.

With no effect:
Clutch was replaced.
Clutch was bled multiple times to whats in total probably a big beer mug of fluid (no signs of any leakage on clutch cylinders).
Gear oil was replaced with Castrol Syntrans FE75, Update: now Toyota LV 75W.
The gearbox was disassembled and inspected, concluding - it's almost like new, except noticeable wear on second gear axial teeth.
2nd 4th gear synchros and a couple of bearings were replaced "just in case".

Before disassembling the gearbox I've read here about probable factory undersized gear selector shaft, but inspecting it there was no free play in it anywhere and no signs of wear on the sides of gear shift heads (notches by which shafts with forks are moved) that probably would be logical to expect in case of misaligned engagement in-between them.
Edit: flywheel runout seems ok (about 0.01mm/.5thou or less), input shaft not rusty/dirty.

Any speculations? Thanks.