The centre speaker should be positioned so that it's leading edge is clear of any shelf or cabinet it sits on and angled so that the tweeter points to where your ears are when you are sitting in the MLP.
The mic should be positioned for the first measurement where you normally sit, at ear height.
d)3. Where should I position the mic for best results?
All of this, and much more, is in the FAQ and 101. I suggest you read through both, especially the 101, before running the new calibration. Link is in my sig.
What happens when the tweeter is above your ear in ceiling?