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Jeremy, glad you figured it out. If you sync your books/notes to the Kindle desktop app, you can also alternately export your notes and highlights from individual texts as raw html with one of their interface buttons. You can then more easily cut and paste into your own site. With a bit of modified CSS magic, you can format it as you like, thus: http://boffosocko.com/2012/06/17/big-history/

Your clippings file isn't bad, but doesn't sync across devices, so you have to export from each of your devices if you use multiple, and they're also time ordered, so if you read multiple things at once, or interspersed, it makes for more processing between titles. There's also a service called https://www.clippings.io/ which may give you some better raw data, though I think they charge a fee for some services.

See also http://indieweb.org/read for other ideas.