R34 won’t go into gear when running

[Idiotwithaskyline]

I have seen a few threads similar and it always seems to be their slave cylinder not being bled properly or pushing the piston enough but I have exhausted this idea and even have a brand new slave cylinder. 
 

I have changed the clutch, throw out bearing and pilot bearing. Not really sure where else to look but assuming I’m gonna have to drop the gearbox and check internals again?

I have not tried starting it in gear from fear of grinding something but it goes into gears smoothly when the car is not running. Any help appreciated.
 

[GTSBoy]

There's another hydraulic cylinder in this mix you know.

[Duncan]

Starting in gear won't hurt anything (except your battery, but no big deal). If you run to say 3,000 in first, foot off accelerator, shift to neutral then hold it against second until it goes in, that will confirm you can shift OK (you almost certainly can)

If you have a second person, have them clutch in while you watch, make sure the slave cylinder rod moves and actuates the fork. That will tell you if the problem is pedal - master - line - slave, or inside the bellhousing.