I'm sorry, I don't understand the question. Pretty much the whole site is indexed, my sitemap in WMT claims to be completely indexed. I used the search queries you suggested to calculate what you're calling the Main Index Ratio for the pandalized site, and 50.5% is what I came up with.
I should point out that I'm not 100% certain that my traffic losses were caused by Panda (of course, nobody really is). Right before the Panda 2.0 update, I had about 3 hours of downtime which resulted in a number of pages showing a DNS error in WMT. I've had that sort of problem before and seen it negatively impact rankings -- but not this badly and not for this long. For the first few weeks I had no idea whether I was pandalized or not, but as time goes on I am more and more convinced that in fact I am.