Of the three methods you mention, #1 is by far the best. If you slot the holes for the engine mount screws, there's always the possibility they will loosen and allow the engine to shift. I guess #3 is the same as #1 in this case, because that is what I would suggest. The fit must be pretty close as it is, just determine how much more you need, and cut a square of hobby ply that will be a little larger all around the engine mount / firewall, drill it to match the holes and glue it in place. I am assuming you have blind nuts on the backside of the firewall, you might need a bit longer mounting screws. This will be just as strong as the original, the weight shift should be minimal, something you can compensate by moving the battery or receiver.

Of course, if you haven't cut the cowl, or drilled the mounting screws, you could alsways just set the cowl back a bit more, as long as it will still fit. I'm guessing that the amount of spacr you need is less than a 1/4 inch, anyway?