I think I understand. It can definitely be tough to work out the right metrics to evaluate a site's search potential, or even the right metrics to report down the line.
To be perfectly honest, I don't think you'll learn much from the numbers you're talking about. There are just so many variables—size of site, marketing strategy, product offering, and specific goals are only a few—that a formula like that can't be universally applicable. Plus, there's the simple fact that in a vacuum a click is pretty much worthless. Who's clicking? Why? Why do you _want _them to? Where are they landing? What did they search for? What are they looking for?
This isn't quite so concrete, but start by thinking about what you want to get from your SEO work. Is it just more clicks? Is it more conversions? Is it greater brand visibility?
Patrick gave a really, really good list of educational resources that might help you wrap your head around everything, but I'd actually recommend starting with the Beginner's Guide to SEO. For the sake of your question, you may want to focus on Chapter 10, Measuring and Tracking Success. That should give you a good sense of what constitutes "success" from an SEO perspective. I also recommend this checklist for a technical SEO audit, which will give you a much better idea of what kind of work you've got ahead of you. (If it looks kind of screwy, it's because of our recent blog redesign. Working on it!)

This generally works out, since there's little if any ranking value in those links—they're not earned—and since the purpose of them tends to be for traffic or for local SEO, rather than for building link count.
We're focused on the blog for now, but it should be responsive as of this afternoon (Seattle). We're all pretty excited.
Just to make sure I'm understanding the issue you're having, is the problem that the tool isn't functioning at all? Or that there are pages you expect to be indexed that aren't indexed?