Sarge, you are making all great points. I think you are essentially saying that you cannot *really* know which KWs and positions they are coming in on, and I do agree with you. In my case, however, I am not even that concerned about individual KWs - more like trends if you will.
I am only going by results of the unsecured searches - obviously there is no way to know which KW sends a secure one, so that's a huge chunk of my traffic that I cannot analyze right there, and there may very well be some surprises there, too.
By the way, there's *some* info you can still get from secure searches - Google continues to set the "cd=" parameter, which is the SERP position/rank.
So, anyway, all the caveats you list are true but they should be working equally for all KWs, and I just can't see how the SERP layout and consequent user interaction would affect the set of keywords. If the keyword no longer appears in my stats after having been consistently there for years, it should mean that my listing is gone from page #1 - never mind the actual position, title or how enticing the description is.
With all that said, I should report that I have started seeing the usual "top" KWs with pretty much the regular frequency in my stats again this morning. This would make it a 48 hr cycle or just about, so it looks like I'm seeing something similar to what diberry is seeing.