While driving, first, second and fourth gears would intermittently lock/freeze up?

Last week my 1997 Toyota Hilux (ta.V.V)
Had a strange fault / issue develop.

When driving, the 1st, 2nd and 4th gear would intermittently lock/ freeze up on me.

Varying speeds, different gears, seemingly at random intervals the car would refuse to switch into gear. Not grinding into gear so much as completely refusing to enter the gear.

I changed out the slave and master cylinders thinking it would solve the issue, but the issue still persists although now it seems to only be 2nd gear that locks out in the same fashion.

So, changing the master and slave seems to have eased the issue so far but not solved it completely.

I did also adjust the free play in the clutch pedal, extending the push rod out as far as I thought possible.

The issue seems to only persist while the car is running, if the engine is off, the gears cycle smoothly..

Also, a friend told me to try coming to a stop, cycle into reverse and then back to second gear and this seems to unlock 2nd gear instantly.

Sometimes 2nd gear grinds a little bit but goes in, others it locks completely out. The problem is intermittent.

I'm worried about causing damage to the gears if I continue to drive in these awkward fashion.

I have checked the transmission fluid and the levels are good.

There was some sludge build up and dark residue in the old master cylinder upon inspection.

I bled the system quite excessively after replacing both cylinders.
Any tips to make the bleeding process more efficient would be greatly appreciated too as 8 must have put at least 1lt of brake fluid through the system during the bleeding process.

I really appreciate this site and the time and energy you guys put in to offering this service! It brings a newfound hope to a budding home mechanic like myself.