The pilot bushing will wear over time. I would not expect it to be binding on the gearbox input shaft if it was not replaced. I suppose it is possible the bushing was damaged / deformed when reinstalling the gearbox and it is binding on the gearbox input shaft.

So you replaced the throw out bearing and pressure plate two years ago and have not driven the car since then?

What happened when you started the car while the clutch was depressed and the gearbox was in reverse?