The easy way to block the boost port is to turn a plug from a good machinable plastic...Nylon, Delrin or Teflon. Give it a light coat of some sort of oil or grease, mix up the JB Weld and apply same into the boost port cavity. Then slide the plug in to form the epoxy to fit with the liner. All you really need to do is block off the entrance to the boost port, not the entire cavity, but whatever happens is fine. After the JB Weld (or similar) has setup, then the plug can be removed. A little cleanup may be required, but it's not a big deal. Don't leave any little protrusions that could break off, tho.
I've been told you can do this with the cylinder liner, but I'd be afraid of gluing it in permanently. Actually, applying a heat gun to the outside of the case should pop the JB Weld loose, so any of this can be returned to stock. The Magnum XLS .36 I'm running (in stock condition) once had the JB Weld treatment. Another approach is to carve a small block of soft balsa to fit, and let the fuel/oil swell it to a tight fit.

Steve