I built S3stat (https://www.s3stat.com/) to fix this opaqueness that comes with using Cloudfront as a CDN and get you at least back to the level of analytics you'd get if you were hosting files from one of your own servers.

RubyGems guys, if you have logging set up already, I'd be happy to run reports for all your old logs (gratis, naturally) so you can get a better idea of which files (and as another commenter wondered about, which sources) are costing you the most.