Showing my ignorance here but why can't I just leave the dowel pin in place?
You can leave it in place as long as the washer on the cam retaining bolt sits flat on the cam sprocket when you tighten the cam bolt.
First picture is 289 with a 406 cam sprocket and a one piece eccentric. You can see the dowel under the edge of the washer on the bolt. If you want one of these sprockets, get it from your Ford dealer. It's hard to find anywhere else.
Second picture is a 430 cam sprocket with a two piece eccnetric. The 430 sprocket is about 1/8 th inch thicker than the 406 sprocket and is the most common after market sprocket style.
Third picture is a 430 cam sprocket.
If you remove the eccentric from a 289 with a 406 sprocket the dowel pin shown just under the washer on the retaining bolt will not let the washer lay flat on the sprocket and will have to be shortened. If you repace the 406 sprocket with a 430 sprocket, and remove the eccentric you will not have to shorten the dowel pin because the 430 sporcket is thicker than the 406 sprocket.
The 430 sprocket with a 2 piece eccentric already has a dowel pin that is short enough to remove the eccentric because the two piece eccentric has a tab the protrudes into the sprocket hole. You can see it under the edge of the washer under the bolt in the second picture.
Hope the pictures help.
James