How to manage a big collection of files with wordpress?

Your best bet is to go with option 2 and alter the DB or use a plugin like http://wordpress.org/extend/plugins/add-from-server/, I can’t imagine uploading 3k large files through a http interface like the WP uploader.

A 3rd and probably better option is to just use a CDN like amazon to host the media files, since WordPress sucks at this type of thing,

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