I have just replaced the box in my VL and it's whining really loudly, it still shifts fine, but is extremely annoying. The previous owner said the box was fine, but due to it sitting for over 3 years without oil in it, the gears may have some surface rust on them, causing the noise. Has anyone had this problem, or something similar before?

the only thing i can think of is fill it with VMX 80 and some nulon box treatment and drive it for a few 100kms see if that helps

Im going to flush the box with oil, but I think the problem is deeper, I think the input shaft bearing is stuffed, because it only does it in 1st 2nd 3rd and 5th gear, when the clutch is out.

It's possible the person you bought it from was full of it.

Very possible ^^^^, but that's beside the point, any ideas?

mine was like that it whined for about an hour(the box had been sitting for 3 years) then it went away,probably just took a while to get the oil into all the gears. put some molybond in it aswell

This is a really loud whine, hasn't gone away, so ive pulled the box out, the oil is pretty brown/gold obviously from rust

if its the input shaft bearing, it will make a loud, almost 'whirring' noise when idling in neutral, which will disappear when you stomp on the clutch

Precisely ^^^^^^ xAsh- The gearbox has been opened and the input shaft bearing has a flat spot in it from sitting for so long. On the down side, it seems the gearbox has got extremely hot at one point and there are discolourations on the counter shaft gear and input shaft gear, im trying to chase a countershaft gear as I already have an input shaft gear, if not, I will only replace the bearing and drive it like a granny until I find another one.