This was resolved. the issue was 4 degrees of chain stretch causing the dowels to be slightly off.

according to the experts here, anything under 5 degrees stretch is within the normal wear and tear range, more than that you will need a new chain and guides .....

Thanks for the response....that is an interesting engine that you are working on. good luck !!

Hi latief,

Thanks for the reply. I understand the chain stretch effect on the basic settings.

But, the point that I was making was that the timing holes only line up every second revolution at TDC.