Right little update.
The clutch has been adjusted. You can feel the "pop" point at the lower half of the pedal travel.

Tried setting the linkage a bit different, made a difference but it is still occasionally notchy going into 3rd/4th. (drivable for now though)
I'm starting to think it might be something internal.

The engine might need to come out again for some other reasons so I shall investigate further then. Thanks for the suggestions.