gteague don't just 'throw everything at it' by loading all your books in one go and instead try loading them in smaller batches (maybe 50 at most?), and give it time to index the books first before adding more. A rogue book can cause the Kindle to get stuck indexing, and if you just chuck more books at it when this happens, it'll just keep 'thrashing around' unless you identify which book is causing the problem and remove it.
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