Hey,

So the shafts don’t sit exactly level on the camshaft bearing caps/journals (the part that covers the cam and rocker arm shaft bolts go through) if I look at it from bearing cap 1 and 5. I imagine that’s because the lobes are in different positions affecting the exhaust and intake rocker arms and in turn putting the shaft in a certain position.

I just wanted to be sure about this before proceeding with the tightening sequence.

 

Correct, because of the cam lobes.