It is possible that since you have replaced the gearbox mount tha the angle that the drive shaft enters the box has now changed, i.e. now applying a different load on the gearbox output shaft.

I had a similar problem; started out as a small whine, which eventually developed into a gearbox failure [rear bearing on the layshaft] Im picking that the clicking/whine is noisier in first gear due to that their is more load on the rear bearings [ output shaft and lay shaft]. As you shift to other gears that load is reduced because you are moving towards the bearing at the front of the gearbox. In my case the gearbox was eventually locked in third gear.

If you have the time, these boxes are very easy to pull down and inspect. Could be easier to replace with a temp box to keep your car ion the road.

cheers Benny