Hi Ben,
This could be something simple, like the gear linkage, or something like an engine steady / gearbox steady not working resulting in the engine moving when you change gear rather than the selector moving in the box.
Check that all engine steady mounts and gearbox steady mounts are sound, you should have atleast one of each, the usual ones are an engine steady above the clutch housing on the right of the engine to the chassis behind the drivers seat, and a gearbox steady from the radiator end of the gearbox to the subframe at the rearmost of the car.
I had an issue where I could get only 1st and 3rd because the gearbox steady snapped,
Places to look at the gear linkage are on the back of the gearbox, make sure that the roll-pins in the connector there haven't come loose / half hanging out. and check un the central channel between the seats that the join between teh original gearbox rod and the extension hasn't come lose in some way.
Simon