Hi Jak,
Here is my typical settings:
Mode: M
T: 1/160 (max sync speed)
A: changing (this is how I control DOF and background exposure), default 7.1
ISO: 200
AF: S-AF
Flash: Fill-in
Format: RAW
In the more advanced menu setting I changed the following:
Button function -> (record) to AEL/AFL
Dial function -> M -> Fno (Meaning that the dial controls aperture in Manual mode)
I played a bit with setting S-AF AEL/AFL mode to 3. This means that half press does not focus, and instead the AEL/AFL button does the focus. This is cool for tricky macro mode pictures, but requires that you remember to focus when you recompose.
I will be glad to hear what worked for you.
Cheers
Nir