Youch! I had a similar mishap (same but different) happen on a higher end Christmas gift project:
It's for a friend of mine that is a music minister. I wanted to do a really nice custom build for him because all he has had the money for is a MIM strat. I used 60 year old cherry for the core, babinga veneer pinstripes, and flame maple on the front & back. The top has two 1/4" layers of flame with a pinstripe in between. Needless to say, a good amount of time in the glueup alone. When I put it on the CNC, I must have bumped the bridge end of the body blank after setting the center line (I still don't know how it happened). So, the center line was out a heavy 1/4" at one end, and tapered to on center at the top. When I realized it, I felt ill...I'm sure Brett knows what I'm talking about.
Anyway, it sat for over a year, and I finally dusted it off to decide what to do. I got semi carried away with the fix, but it turned out OK, and thats the goal. I inserted a tapered wedge of crotch walnut that goes down to the first babinga pinstripe, then inlaid a similar scroll design that matches the neck inlay.
I guess what I'm saying is don't fix that "one of a kind" top with a plug that makes people ask: "what happened here". Go over the top and do something that in that area that makes people say "wow...that's pretty cool". Even if it means shelfing it for a while.