Hi Andy,
AHA
Look carefully at the inner splines in the clutch cush drive spider
They are fractionally below the flat surface of the rest of the components
this is whats causing the binding up, allowing the centre move towards the chain wheel when tightened up
Glad the thinner thrust washer will work as this is an easier way out
I normally align the primary drive before fitting the inner primary casing,
I use a length of 8mm square steel bar (key steel) to check along the rear of the sprockets
If each of your measurements oppose each other, then you cannot be far out
HTH
John