Leave the gearbox in situ - it's the clutch and spigot bearing alignment - as Martyn says - use a alignment tool before fitting engine into car or you can also use a hacked off input shaft off an old gearbox.

Other than that - if you have checked alignment - put a spanner on the crank lower pulley bolt and use it to jiggle the crank whilst having the engine in the car with the gearbox partially installed (ie. when it won't quite slide home) - you should get the appropriate spline alignment on the clutch plate and it slide into position.

As Martyn says - quite often at this point you wonder what all the fuss was.

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