From your description it's most likely the nylon bush at the tip of the shifter (inside the gearbox) has disintegrated. You need to take the shifter out either by removing the circlip under the rubber boot, or by unbolting (6 bolts) the top cover and removing the shifter with the cover. Circlip is probably the most direct, but can be a bastard without the right tools. Once out, there should be a small plastic bush at the tip of the shifter - I'm guessing in your case it'll be gone (inside the gearbox, but don't get too concerned). It's only a few $$$ from Nissan, and is common to local R31 Skyline gearboxes.
If that's not the problem, other possilities are things like selector roll pins, but that gets complicated (gearbox out).