Error 99 as far as I remember (had it a LOT on a 300D I had years ago) also involves the lens to camera frame sensor - the series of brass "dots" on the lens and the pins on the ring. Canon tech told me to clean the dots on the lens with a pencil eraser (the small one on the end of pencils). It worked - seems the brass contacts get slightly corroded.
But, the Err99 is a catch all error, so trial and trial again will eventually find what's up.
Never had it on the 40D (4 yearsold) and not on the 5D
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