The dowels may only be case hardened. If so, you might be able to grind through the case with a die grinder and drill and tap from there. It's not going to be easy. Getting a machinist involved will probably make the most sense.
Note: If you break off a drill or tap in the hole it'll make matters much worse.
If the engine is out of the truck, it could be set up on a large horizontal boring mill and the dowels could be milled out with carbide. This option will not be cheap.
Sometimes, the smallest problems can create the biggest headaches.
Good luck.
John
