>But why? As I understand it, the light comes in the lens and >most of it is reflected up to the eyepiece. The rest of it, >since the mirror lets some of the light through, goes to >anoter mirror behind the main mirro and at a 90 degree angle >and is reflected down to the focusing sensor on the floor of >the camera. When the picture if focused, the sensor tells the >lens to stop focusing. If the distance the light travels >between the back of the lens and the focusing sensor is not >exactly the same as the distance it travels between the back >of the lense and the imaging sensor, the focus will be wrong. >If there is something wrong, how is changing the lens going to >affect this. If the focus is right, how is a different lens >going to mess it up? What does the lens have to do with any >difference between these two distances?
I think that we are talking about two different things, image quality of the lens and Auto Focus.
IMAGE QUALITY: I think its the quality of the lens glass - placement of the lens elements I don't know - Like you said it sucks. We would expect more from an $800 lens. It doesn't affect the focus of the camera, its just that at some (maybe many) focal lengths and distances the 18-200 lens is not very sharp (your question "Where is the focus"). There are quite a few photos that I took with that lens which I have been very disappointed with and kept thinking it was me or the camera.
AUTO FOCUS and what may have pulled your camera's auto focus: Items of high contrast near your intended subject of focus can influence your camera's auto focus. In your first photo of the flower from your earlier post, I think what happened there was that the brighter light and difference in contrast pulled the focus to the flower pedals behind the part of the flower you intended to focus on.
Sometimes manual focus works better when there are items near your intended target that have greater contrast, or moving to get a darker background. Earlier this summer I was photographing day lilies and to get the front for most stamen and the others behind in focus, I had to use manual focus because the camera kept shifting focus to the stamens that were closer into the flower (more contrast) and I wanted to keep a wider aperture to keep the background out of focus.
Looking at that flower and the petals "in focus" in your earlier photo the 18-200 still did not produce a crisp fine image of the detail on those pedals. I am amazed at the detail that the 18-55 and 55-200 "kit lenses" show, and bummed that I spent $800 on a lens that I have been more often than not disappointed in.