First, the holes in the engine flanges aren't threaded. You can either drill completely through the mount arms, and bolt the engine in place with washers and nuts as you indicated, or you can drill and tap the engine mount (which is glass-filled nylon) for 4-40 bolts. That works for me, but some people don't recommend it, preferring bolts and nuts.

Second, placement of the engine on the arms should be more a function of balance than distance of the spinner from the nose of the plane. If the engine sticks out more than 1/4", so be it--it's not as important as a well-balanced plane.

The thrust line of the engine (how high it sits) is indicated by the bottom of the engine flanges. On my SSE, this is almost exactly at the most forward point of the fuse sides. Your pictures of the mounted engine look correct. As for right thrust, if the engine sits square on the mount (i.e you drilled the holes nice and even), the engine will be correctly aligned. A little off isn't anything to worry about.