I was hoping someone alittle more would respond but here goes...
I recall mine not lining up exactly too. Tried leaning up and down and went with up as it was the closer of the two. But as I was using a used chain, that would make sense.
make sure the cam and gear interlock pin is up at 1 o'clock and that the crankshaft is still aligned with the mark in the case. Rotate by hand to confirm.