I haven't seen the offending manifold, but would say that if there is enough metal to provide seal for the O rings, there is enough to tap and install some plugs.
Remember that pipe threads taper and bolt threads don't when you make your choice. Allen head set screws are a good choice for plugs if you choose to use a bolt thread. Pipe threads with a taper tend to seal better. Some Teflon tape on the threads of the pipe threads would be a good idea. Use LockTite on the set screw threads, and be sure to give it sufficient time to set. A trip to Ace Hardware, Home Depot or Lowes is in order to find what you need.