In a moment of clarity I think I have found the explanation for why my rear wheel is shifted 1/8" off center (to the right) in the rear swing arm when installed with what I am pretty sure are the stock spacers. It would appear that the swing arm forks, the lower shock mounts and the upper shock mounts (on the frame) are all shifted to the left by aprox 1/8'" from the chasis centerline. This becomes fairly obvious if you run a string line from the center of the headstock back along the center backbone and out the back of the bike (see attached Pic . Honda then shifted the rear wheel 1/8" to the right of the swingarm centerline to bring the wheel back into the center of the bike's chasis. I am not quite sure why it was necessary for Honda to do this shift (perhaps for packaging all the parts or for chain clearance etc) but it seems that I was foolish to doubt their work and also to have enough confidence in the meaning of my earlier measurements that I spent a few hours milling a shortened left spacer (I had an extra) and a thin secondary rt hand spacer. My installed handiwork can be seen in the Pic as the rear wheel is obviously too far to the left, although it is now perfectly centered in the swing arm.
. . . . . . . .
So Yankee you were right when you told me that my rear wheel only appeared to be off center! Thanks. . . .However, I would take a closer look at your rear wheel spacing because if you are running a stock 78 frame, swingarm, and rear wheel with that extra spacer on the left then you probably aren't centered up. Maybe you have an earlier wheel?
Well now that I am done chasing wild geese, all I have to do is put back in the stock spacers and then set up the straight edges or stringlines and point my rear wheel properly at my front wheel. . . .