You have to remember that the layshaft taper bearings are fully immersed in the oil, and they don't have that big bellhousing to amplify any noise, so regardless of the preload, whether too much or too little I just can't see those making the kind of noise that you're getting.
Either way, it sounds like (did you see what I did there....) the box is going to have to come out and be dismantled again to see what's going on. If it's really that noisy then the cause should be easy to find when it's in pieces.
One thought, did you fit the shim in front of the first motion shaft bearing, or if you had a bearing that was covered one side, which way around did you fit it?