If the box fits, the clutch is lined up enough. it only needs to be close enough that the box physically bolts on, then the 1st press of clutch pedal perfectly aligns it.
However, alignment isnt your problem, you haver the wrong clutch/gearbox. 2y box has a larger input shaft than the 8v boxes, so the splines on the 8v box wont engage the 16v clutch. Gearbox off again I'm afraid
