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One additional thought: perhaps the error message refers not to anything within your source NCX, but a problem with the resulting waypoints that are supposed to be built for the book.
I'm not sure exactly how they're stored internally, but perhaps trying to generate whatever records are needed to quickly get to the farthest points in a 56 meg-equivalent book is what's giving the "index" error, if it's done in some way that overspills the 255-byte limit for however Mobi files reference their waypoints. Especially if they do it in some sort of special supplementary fashion so the entire book doesn't have to be loaded at once before the navigation is accessible.
Depending on whether it's a conversion-time error and KindleGen is just plain choking on a large input file, or a limitation of the overall format, you may or may not want to try splitting your file up and referencing the various parts via an OPF and see if that helps any (assuming you're not already working from split files to avoid having to deal with 52 megs of text at once).
The other possibility that I'd suggest is that perhaps you have a very minor error in the NCX file. I discovered that if I accidentally put in a superfluous empty end-tag, KindleGen would completely ignore the entire thing without even giving me an error message.
But you do seem to have gotten error messages, so that's probably not it.
Anyway, I hope you manage to find a way to fix whatever it is that's doing it.
ETA: Maybe check your version of KindleGen? They did update it at some point to support Kindle Audio/Video and correspondingly larger image files than the older Mobi tools allowed; maybe they upgraded the overall filesize it could handle, too.
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