Have been in this car, story checks out haha. Very odd.
When was the clutch done, it sounded more flywheel/clutch/spigot/thrust bearing location but super hard to tell. If the thrust and spigot bearing were not replaced with the clutch it could be that? But I think you might be right in assuming its something going bad in the gearbox... It might be cheaper to bin the trans and pickup a lower milage one. 5 Speeds can be had for $300-400 these days and then its just a straight swap, rather than full teardown and diagnosis.
Could flick the old one off as noisy but functioning to get some cash back.
Hope others on here can chime in as i'm mostly lost on this too