just got a 40D. i had hoped with the "improved" autofocus of the 40D, i would get better focusing with my 100-400 +1.4X with last 3 pins taped.
but autofocus with the combination seems to be unusable (it tries but rarely acheives focus even in good light)
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Which shows that Canon disables AF in this situation for a good reason, not just to make life harder for users of its cameras!
AF sensors need a low enough aperture ratio to operate reliably or at all, and typically the limit is about f/5.6 to f/7. A few high end cameras work to f/8, but I believe that this is done by having several AF sensors at some locations, one working to f/8, others working only to f/5.6 or f/4 or even f/2.8.
What not just make all AF sensors work to f/8? Because an AF sensor with lower minimum usable f-stop (say f/4 instead of f/8) is faster and more accurate with lenses having minimum f-stops within its operating range.
(This is one reason why I prefer an SLR system with enough sensor resolution to let me use lenses about f/4 or faster (and certainly f/5.6 or faster) most or all of the time: having to use longer telephoto lenses with higher minimum f-stops like can be bad for AF.