I don't know the answer to 'What is the spec on the minimum depth of scratches on a flange so that the leak rate is less than XXX Torr/liters/second?"

But here are a couple of vacuum texts which might have it:

1. "Fundamentals of Vacuum Technology" PDF from Leybold
2. "Vacuum Technology" by O'Hanlon (this is THE standard reference - don't know if there is a new one)
3. "FOundations of Vac Sci and TEch" by Lafferty sounds promising, but I've never looked at it.