Murrey. I had this problem and what I did was to go along to my local engineering shop and asked them to check it out. They can put the cases onto a surface table and then using a vernier height gauge they can check it out. The datum has to be the crankcase mouth, because if that is not perfectly in line the cylinder base joint will leak. Next the sump plate faces have to be correct or the sump plate will leak oil. Thirdly as you have said the bores must be in line. This type of work is quite normal for an engineering machine shop and certainly in the uk ,if you let them fit it into their schedule I am sure they will help. all the best with it Goldy