Are these holes or are they true counterbores? A counterbore would be a section of larger diameter at the top of a hole of smaller diameter.
If they are true counterbores, it is pretty easy to make a custom tool to enlarge them if you have a lathe. Take a piece of steel and turn it to the diameter of the smaller hole. Then drill a cross hole through it in which you will insert a HSS cutter that extends to the desired larger diameter. Drill and tap an axial hole at the end of the tool to hold the cutter in place. When you are done, you will have a tool that looks and works like a fly cutter, but has a positioning "nub" at the bottom.
For the actual cutter, you might use a cutoff section of a half round drill bit.
I've made and used such a tool to cut a two inch diameter taper in an aluminum manifold. It worked just fine.
Kenneth Lerman
55 Main Street
Newtown, CT 06470