Thank you again for the response!
So am I understanding you correctly too in that each camera will be calibrated differently, so to speak, and some 5DII's will have more shims than others depending on how they are manufactured?
Pretty much. Things get even more complicated when you have a 100% screen, like the Mk III. Lots of hand calibration.
The dust you saw was probably on the bottom of the focusing screen in the first place, btw.
I feel so much better now. I can go out and use my camera and finally enjoy it after all this useless tinkering!
One last question, though: Is there any particular symptom that will show to make you want to add or remove an extra shim?
If you manually focus, and when you are certain the image is sharply focused, but the image is not in focus, that indicates a problem. Once its properly calibrated, if it goes out, something is wrong and it needs to go to Canon, they do not go out unless something has broken.
Normally, a change in shims is only required when a different screen is installed, and its a slightly diferent thickness. This seldom happens unless you were to install a 5D screen in a 5D MK II, for example, and then they normally come with a shim.