Here is a incomplete list of four reasons for the noise;
1. Bearing failure. Worn, pitted bearings make noise and produce heat.
2. Worn constant run gear teeth on the input and the front gear of the countershaft. These are the teeth that the power goes thur in all gears except 4th. These gear teeth fail because of--- low oil, wrong, poor quality oil, or just run too hard-also known as overheating. It will usually require a trained eye to catch the failed teeth. The technician must be very careful to complety examine the complete gearbox.
3. Excessive mainshaft end play-check the retainer plate for wear. This keeps the gears in line.
4. Cleanliness, Cleaniness, Cleaniness.......................
It sounds like this trans had bad bearings and worn gears. The failed bearings were replaced which placed the worn gears in a new pattern and the noise went away. It came back because the worn gears transferred more metal and the noise once again returned. The noise returned the third time because of left over metal in the gearbox which did further damage. How many times can I say Cleanliness...........hard to take a clean bath in dirty bath water 
Were all the bearings replaced? or was it another slam job. Did the technician blueprint the trans and correct the W56 shortfalls? Was the oil delivery tube removed and cleaned? Sorry about the technicians job but it sounds like another slam job. 
Hey marlin can I pick your brain for a minute?
So I have a related problem but also a question, would an over tightend rear output flange nut on the T/case make the gears rattle???
