I am afraid that you look to have assembled the clutch shaft to the fork incorrectly. The manual specifies how to do this, making it clear that it is possible to get it wrong (reading between the lines!)
What I would be inclined to do is to drill a second set of holes in the coupling sleeve to accomodate the incorrect position of the shaft. This is not going to be easy, as the sleeve is hardened, but it is probably easier than removing the gearbox!
John
JDNSW
1986 110 County 3.9 diesel
1970 2a 109 2.25 petrol
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