Haven't actually looked at a kit but from the photo it would be fairly easy to change it to a side mount. Depending on how it's designed I would either replace the hardwood engine bearers with hard balsa and cut them off at the front of the firewall or eliminate them altogether. If the firewall is 1/8 plywood, make a duplicate to end up with a 1/4 inch thick firewall and use an RC engine mount turned on it's side. Is the cowl built up from balsa or a preformed part with a cutout for the engine already cut. In either case it wouldn't be too difficult to get the cutout in the right place.
That is what I would do simply because I am completely convinced they do run better side mounted and feel it's worth the trouble, however many have ran 4 strokes inverted and seem to be happy. You just have to make a decision, is it worth the trouble for you?
I wouldn't worry about the vert CG nor would I even think about modifying anything on the Saito but the intake..
I do think the Saito 40 is an excellent choice for that airplane..