The pilot bush generally only does anything when the clutch is disengaged (pedal depressed) and only locates the shaft centred when the pedal released. If it jumps out of top gear the pilot bush is most probably the culprit as the input shaft, crankshaft and gearbox output shaft are not in a straight line.
If you have a growl in 2nd gear only I would be looking at the gears related to 2nd gear only, if it growls in all gears other than top check the laygears or cluster shaft (the lower shaft) and associated bearings.
In any case the only way I know of to fix it is to remove the gearbox from the vehicle, not an easy exercise and possibly not cheap to fix.
