Rob, the Scammell 6 speed is a law to itself, it is almost too clever for its own good. When I bought my Explorer it had 6k miles on the clock but it was difficult to engage 3rd from 4th. When I stripped it down the needle bearings had vanished from one journal and the large mainshaft gear was floating about so much it had almost machined its way through the casing and destroyed the shaft. Noise? quiet as a mouse in all gears. The replacement unused REME re-build was just like yours, howled like a banshee in top.
A friend of mine is an LGV fitter with a large outfit that owned a Highwayman which howled in 6th. They tried everything, had the 'box out 5 times, new gears, new bearings, different gears and still never fully resolved the problem.
Bear in mind they are straight cut gears which are prone to whine and 6th is a serious overdrive, 0.62:1. The actual specs for the 'box call for very tight tolerances, typically the diameter of a needle bearing journal is given as 1.7313/1.7308" i.e. half a thou. although whether this was achieved in production is debateable.