I would figure out how to make your pages as flat as possible (I'm assuming they're in bound books somehow?) and then, as already stated, use a tripod to keep your phone level. iPhones have a level in the camera as an option, so you can set it up and then use a remote to take the photos. That way you're not moving the camera at all, which will get you a crisp image.
As for an app...IDK. I would just take the pics and then use something like Bulk Name Utility to rename things/change metadata. You'd have to change by month or year or whatever, but that might be quicker than doing it page-by-page.
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