It's the spring in the scissor gears(in the primary gear) that keeps the tension on the gears to prevent backlash...so the misalignment is normal when apart. This was mentioned in a thread awhile back. Seems a screwdriver between the gears is used to align things.
http://www.hondashadow.net/forum/72-technical-discussion/120530-engine-rebuild-more-14.html
http://www.hondashadow.net/forum/72-technical-discussion/120530-engine-rebuild-more-14.html