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Ideas yes, plans no. Hugin gets you about 90% of the way there already, although it's rather awkward having to save and load pairs of frames. Copy/paste into Hugin would make it a lot easier, but I doubt it's something they'd implement. I was going to incorporate a control point GUI in something else I'm working on (which may or may not ever see the light of day), but I ended up steering from a two-pane GUI and it's a bit complicated to reimplement now.
StainlessS - I think it was him, he's usually the one with the crazy ideas - has previously posted scripts for using AutoHotKey to record clicks on a VirtualDub window, I believe. That could work with a stackhorizontal clip of the two videos, although I have no idea how you'd extract which frame you're on, nor would it give any visual feedback like Hugin does.
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