I have replaced ARF engine mounts by doing the same thing, knocking out the blind nuts. To hold the new mount, I used the brass threaded inserts. Great Planes and DuBro, as I recall have them. You can fill the old holes with 1/8" dowel epoxied in. If your holes are going to overlap, you might want to angle the engine slightly to the side.

If you are using the square back Hayes mount, you can grind away the nose gear "hole" reinforcement and move the engine a little more to the rear.

In addition, after you mount your engine, take the rudder servo out and rubber band it right in front of the fin and check the balance. If this does it, you can cut a hole for the servo, CA a little piece of 1/16 ply under the balsa sheeting and hook it up pull-pull with coated fishing leader. I have attached a photo of my SK/50 that I made this mod on to balance when I used an OS .61 instead of the recommended .46.