Purchased a nice/clean 99 Tracker 4x4 5 months ago w/ 78,000 miles from someone who towed it for most of the miles. It recently started havinga a grinding noise when it's in neutral with the clutch out. The mechanic and I immediately thought it was the throwout bearing - after installing a new clutch and bearing ($550) it still made the noise. The mecahnic said that it's probably the 1st gear so he went back in and replaced that gear and the ??shaft?? in there, put it back together and it is still making the noise. Luckily he didn't charge me the 2d time. It shifts smooth and drives great (little rough idle and getting only 20-22mpg - probably needs new plugs and wires?) Any ideas on the noise - pretty loud with the clutch out, goes away immediately with clutch in all the way.I tried to download the bulletin mentioned in another post on the 99 transmission mesh synchronizer but got a bad link.
Well it sounds like you have a the vacum for the four weel drive is trying to engage when it is in nutrial and that is where the noise is comeing from. I just think the person you took it to is just trying to make some money off of you