Hi Leif,
I posted a reply a few hours ago, but it's disappeared! So here it is again!
I find it strange that you have an aluminium spacer in the box, I think that normally in a gearbox the spacers etc. would be steel or bronze.
Regarding the sprocket alignment, I have no idea! But did you replace the mainshaft bearing? Maybe it needs tapped in a little further, or is slightly thicker than the original. The other possibility could br the clutch centre, you could make sure it's a good fit by smearing a little valve grinding paste on the taper and turn the clutch centre a few times to make sure they fit together correctly. Or as you say possibly dodgy pattern parts.
This probably won't help, but good luck, hopefully someone out there will have the answer
Webby