Update...
I changed my fork oil today; naturally I worked on the fender alignment!
I believe that the primary problem with my fender was that the covering tubes weren't properly aligned. The scratches on the tube and fender show that the inboard external side of the right tube was rubbing hard against the fender; when I removed the fork, I could see that the outboard internal side of the same tube was rubbing hard against the fork - hidden damage I couldn't see until I removed the fork. The tube was clearly "leaning in" at the bottom.
Because I couldn't figure out how to remove the covers without dropping the stem, I decided just to see if I could properly align the old parts and save the new part installation for another day. I have since heard from Ron Greene who says there is indeed a trick to removing them without dropping the stem, but I haven't spoken to him yet! Anyway...
I used Scotty's trick of cutting up a cardboard paper towel roll - I ended up stacking them to force the tubes into position, tightening the pinch bolts, then removing the cardboard. After two or three tries, I got them both so two layers of cardboard fit with even friction all the way around.
Then I put the fender on - it looked better already, but it is still very difficult to tell from the top. But since the front wheel was off, I laid on my back under the fender and looked up - perfect view! It's easy to visually compare the clearance on both sides from the bottom! Here's a pic:
My two eyes are far enough apart that it's easy to see both tubes above the fender, but the camera has only one eye (the lens), so it doesn't see both sides at the same time very well in the above.
The right tube:
The left tube:
Since the fender stays seem to have very little play at the bolts which hold them to the forks, I tightened them up first, which got me close. The fender was still leaning a bit right, so I wedged a dry, some-what hard kitchen sponge between the fender and the right tube, which forced the fender left. I tightened everything up, removed the sponge, the fender sprang back just a bit and now seems to be right on center. I can't see any evidence of rubbing, but I couldn't see the actual rubbing before anyway, only the resulting scratches. I'll put some tape or something on the fender and see if it rubs, but I'm pretty confident I've got it lined up...
By the way, the nuts that go on the screws that hold the fender to the stays are a strange size, on my bike at least. No metric or inch wrenches or sockets I have would fit it. I had to use an adjustable wrench...