Progress report...
I spoke with Roger at moviestuff about the difficulty I had aligning the camera with the new, enlarged gate, and the resulting discoloration at the corners. He suggested that I experiment with removing the main lens and positioning it closer to the projector. I did that - it required quite a bit of fooling with it, and then drilling some new screw holes in the mounting board - and it worked very well.
As a result, I recaptured reel 1. I'm more comfortable now with this new capture, the image is solid and consistent across the entire frame out to all four corners. So there is now no need to mess around with trying to fix the corners in post.
Besides, that's time better spent playing with videoFred's avisynth script that Mothr turned me on to! I downloaded MVtools, and the magic script, and am anxious to see if it's for real. Heck, if it really works I could even run the original Puggo edition through it, since it's still frame-by-frame.
The old sound sync should still work fine.