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Do you have any evidence to point to this ~1000 cookie limit?

This is a bit dated, but it makes sense that there is a set cookie limit: http://www.ghacks.net/2008/08/16/browser-cookie-limits/

In Chrome it's 3300 [1]

The cookie preferences they mention for FF are no longer in the default list at about:config. I wonder if they've gotten rid of the limit altogether.