Don't worry about the pins not being there, people run without them all the time. The problem I was referring to is because new manifolds generally aren't drilled to clear these pins (which locate/retain the manifold end seals), so if you don't remove them or drill the manifold for clearance, the manifold can "rock" on top of the pins and not sit down where it belongs- which could cause a sealing issue. But if your pins were removed, that probably eliminates that possibility.
