Nothing wrong with popping out the blind nuts, filling the holes and remounting where you need to. I use a hardwood dowl, drill the existing holes out accordingly, and plug away. You could add a piece of ply backing too since you're using a gasser. Then find the best fit that will work for your engine while leaving as much space between the new holes and the repair as you can, though not to worry if they are close.

Not looking at the plane I'm not 100%, but I imagine that the holes are offset to make up for the engine thrust. The engine will be angled to the right a couple of degrees, so to keep the spinner centered in the cowl, they off set the engine.

You want to dry mount your engine on the mount, then dry fit that on the plane to line up with the cowl, otherwise it will look bad. Just do a good job plugging the necessary holes and put the engine where it needs to be. You may only have to plug two holes, maybe all four, depends...

Good Luck!