I've had a bit of time to think about the engine and plan what to do next with it. There is a slight taper in the bores, but I compensated for this by making the pistons and valves to suit, I now plan to lap out both bores until they are spot on parallel and both the same size. I will then make new pistons and valves, it may not help the running, but I won't know until I do it.
All my time lately has been taken up with selling my mothers house and clearing it out after she had moved to aged care, but this is nearly finished so I will have some spare time again to work on the engine.
Paul.