Owain, you say;
"I have the layshaft thrust washer between the last sprocket and the layshaft bush that sits in the inner cover"
That thrust washer should be the other side of the first gear pinion, between the pinion and the layshaft shoulder, chamfer towards the layshaft shoulder.
Photo is from a swinging arm box but the thrust washer position, indicated by the arrow, is the same for both plunger and swinging arm.