That worked.
With my previous GPS accuracy comment aside (but note that 3m is actually quite a bit), the JC Penny part looks like more of a timing issue (as boblui mentioned above) rather than positional.
So if it was synced at one part, then got out of sync, then you're talking about aircraft speed not being 100% the same throughout the entire sequence of both clips. And that's probably not fixable within a waypoint mission, because it's my guess that it wasn't designed to be that accurate. That is, the speed of each mission could differ due to a lot of factors.
If I were doing this, I would a) do several takes of each mission (several daytime, several nighttime) to see if one take syncs up better than the others; and b) look into time-warp adjustments in your video editor, if it has it (I don't know if it does, but I would go looking for one, even going up the video editor's own forum to ask for one, if they have one).
But overall, I think the effect looks cool.
Chris
PS: the hourglass issue could have been at my end, if another user could view it. but thanks for the youtube link.