This may not be entirely your fault. I've had rear wheels that I've built up seeminly de-dish themselves by a few mm after their first ride or two. I suspect I hadn't fully bedded the drive side spokes as I was tensioning / stress relieving the wheels. After a ride or two, the spoke heads bedded in a bit better, and effectively reduced their tension, allowing the wheel to move back over a bit.

Regarding your alignment problem, it's actually pretty common for the dropouts to be at slightly different heights. No problem centering a perfectly dished wheel between the chainstays, but the top will be off at the brake bridge. It's the one aspect of frame alignment that can't be fixed after the fact on an alignment table. (If the chainstays are slightly different lengths, you would never know it on a horizontal dropout.) That's one of the reasons no one really used vertical dropouts until the 80s. Production (and even most custom) frame building and alignment just wasn't precise enough to guarantee you wouldn't have the wheel way out of whack. It wasn't until the Japanese got their act together, and pressured everyone else to up their game that you would see vertical dropouts on production frames.

On one or two bikes that I cared about, I've actually gone through the trouble of heating the dropout / seatstay junction on the higher side to reflow the brass, and then tweaked the dropout back to where it should be. I would only consider this on a frame destined for re-paint, and I wouldn't try it on a chromed dropout / seatstay.

One last point -- you might want to consider re-dishing your wheel back to where it was. All that the bike cares about for purposes of riding no-hands is that your center of gravity is right in line with the contact patch of the front and rear wheels. With your wheel slightly off in the frame, a perfectly dished wheel will in effect put the tire in the same spot as a frame with a crooked rear triangle. You might find it doesn't ride no-hands quite as well now that you've "fixed" the wheel. Really, the point of a perfectly dished wheel is so that you can interchange it with any other, on a perfectly aligned frame. If the frame is off in ways you can't fix, you have to choose between easily interchangeable wheels, or a functionally mis-aligned frame. (It might not be enough to matter, but keep in mind that the goal is getting your body right between the wheels, not necessarily in having every component perfectly centered and aligned.)

I've done the same.

Sometimes I think we're twin brothers of different mothers. I've often thought that you could intentionally offset a frame's rear triangle and reduce dish for a stronger wheel. You'd have to accomodate chain line, and make sure the crank arm doesn't hit, but it would be an interesting design proposition.

Thanks Gugie, that's high praise coming from you. I like to think it comes from a unique combination of having a machine / fabrication shop, and a border-line pathological desire to "make it right". Sometimes it's even a good thing :-)

Kind works, thanks! It'll be great to meet you at Eroica, we can talk about some potential projects we can work on together.