I'm rebuilding my Kubota B5100E tractor engine. I've only worked on engines with timing chains or belts never gears with an IP pump. When I line up the 1 mark with the crank and center gear, the 2 mark with the cam gear and the 3 mark with the IP and rotate the engine they are no longer lined up. I've set it 3 times and it still is off. However when I rotate the engine the cam seems to be opening the valves correctly. I don't know about the IP. When I took the engine apart it was running and I noted that the marks were off. Is this normal and will the engine run correctly when I'm done? Thanks for any advise.