Bolt the manifold back on, use it to guide the drill & keep it straight.. If you have access to a lathe I like to make a drill guide bushing, take round stock slightly to large to fit the bolt hole in your manifold & bore a 1/8" hole through the center of it, then turn the outside to just fit the bolt hole... Now you have a guide that will center the drill & keep it straight....

BTW you bolt is borderline to deep in the head for the weld a nut trick...