Dave,

The 1/2* difference might be the way the incidence meter is being positioned. An old-hand taught me a long time ago that the meter should be facing the same direction when measuring both port and starboard wings. In other words, if the meter is facing the fuse while on the port wing, then it should be facing the outboard wing while measuring the starboard. Most folks have the tendency to face the meter towards the fuse reguardless which wing it's on. You wouldn't think it should make a difference, but often times it does.

If you're not facing the meter in the same direction, you might want to try it to see what your readings pan out to.

Concerning your dowel rods and holes. You can over-size the holes to obtain the proper wing position. Once you have the wing where you want it, place a new piece of plywood, with the proper sized hole drilled, in front of the former. Align it so that the dowel is through the over-sized hole and inserted into the new ply at the correct position.

I hope this is of some help, cause I know these alignments can be very frustrating.