a manual won't shit unless it is at 4k rpms?

strange...

i'd start with the easy stuff,
enough fluid
good fluid
master is working
lines aren't leaking
slave is working
gear lube in the tranny, enough of it, is it good?

pretty much anything beyond that and you'll have to start taking things apart.
It almost sounds like a synchro issue, in which case, it could just need the gear lube changed, or it could be jacked up.