I didn't quite find what I was looking for, but I figured it out.
What I did was start a 20x20 cube print, with different color infill and hit print.
I watched the layers, and guessed how much it was off by.
I paused the print, sent the G10 P1 Yx.x offset code with my new number for Y, and a M208 Ux.xx for offsetting the second extruder in X.
Then I homed X, and resumed the print. I would let it run a couple layers, then look at what needed adjustment. Then I repeated this process until I was happy with the result.
It was as "Live" tuning as I could figure out. It wasn't so bad.