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If this is to eliminate false positives, why is it necessary to count all the negative hits?
Doesn't the presence of just one false hit exclude a document?
If so, the simplest optimisation might be remove the /g;
Presumably, this is just one example of a generic problem?
Otherwise, if you'd just left the regex running from the point where you posted your question, until you posted your follow-up, you would have processed a little under 1 million documents of the size of those you've linked.
If it is a generic problem of optimising complex regexes, then you'll need a programmable solution.
Whilst it may be possible to hand-optimise the supplied regex to cut runtime, you'd then be faced with having to do it all again for the next set of false matches.
Perhaps the next simplest solution would be to multi-task your processing of the documents.
Spread your load across the 4 cores of a typical current machine and you can cut your processing time to a 1/4.
Purchase a $100 of Amazon's EC2 time and cut your processing time to 1/100th or less.

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