Hi what i mean by photos is of the crank the crank case view FROM the top where the cylinder fits on the see if the crank is over to one side or if the crank is to wide ??
Did you have the Crank rebuilt
Is it the same width ??
The way i buld my pilot Engine is
1 Press bothe the bearing on to the crank shaft and then CHECK for ture.
2 Warm up the RH case then lower the crank in to the case, let it go cold.
3 Put the 2 dowels in and the gasket on to the RH case.
4 Warm up the LH case and DROP it on to the RH case let it cool then put all the bolts in.
5 Strike the crank so that is in the centre of the cases, now go and CHECK the bolts for Torque.
This way you have not put any stress on the cases or on the crank, If you don't have a press you can put the bearings in some twostroke oil in pan and boil them to get them hot and then DROP them on to the crank shaft.
Hope this helps .