Rudder, Pintels and Gudgens

So, the new rudder doesn't match up exactly. With the bottom pintil lined up it fits above the keel, but the other two pintils are off by about an inch. Guys have been telling me I'll have to cut the rudder up to make it fit and I'm trying to figure out why I shouldn't just plug the top two gudgeon holes and redrill them to fit the way the rudders are made? Seems like the right path, so that and the rest of the keel work are next.