Are you sure it is possible to calibrate auto-focus? I think it works with contrast, it adjusts focus where contrast is best, so that shouldn't need calibration. Estimation of subject distance could be calibrated, but there is no impact on quality of focus.
I don't know if there is a diagnostic mode, but if there is I'm interested!
Maybe you should try asking Canon (where did you have your main board changed?), they certainly have better knowledge of this kind of things, and keep us posted because we are interested in!
