Stan, I use a router with a bearing on the base and a straight plow bit. Therefore I can do the binding first and perfling last. As the bearing is quite far down from the bit. If I used a bit c/w bearing then I would probably do the perfling first and the binding last. As the probability of the router climbing and the bearing slipping into the binding plow is quite high.
If your bearing did not ride into the binding plow then the possibility is that your top was starved of glue at the kerfing contact point.??? Could that have happened? Your sides should not be that thin, that they would move do to bearing pressure.
If I removed my top and had to redo the kerfing(provided I didn't break it taking the top off) then I would resand down the top edge until the kerfing was flat again.Or at least I would in a perfect situation. It would all depend on how badly scarred the top of the kerfing was. Your guitar side depth should be able to stand being taken down up to 1/8" (I would think). You would have to make allowances for the neck fit and so forth. (Your top ledge will be a bit smaller if you get as far as the slope on your kerfing sides).
Sorry to hear of the frustrating problems that arise out of unforseen problems.
But hopefully you can use the top on something else and glad to hear you have nother top to install. Hope new top goes better with no problems. Take care.