Let me see if I can break down your concerns ...

Assuming the "amounts paid" you reported were net-after-taxes, base points are given on room rate booked before taxes; however, taxes and tip are included for points on incidental charges. So, if you paid $1,393 before taxes for the long stay and your last night, the points are correct.
I suppose New Years Eve did not end up qualifying for the Q1 2012 promo, so no 1000 points for it. The Q4 bonus was set up to allow for stays with check-ins in 2011 to be qualifying, that's how you got those double points.
The 5K weekend may, indeed, have gotten lost in the shuffle.

Finally ... you were VERY lucky to have received those variable BA miles! A back-to-back stay at the same property is one stay, regardless of checkout between. You should have gotten a flat 500 miles for the whole 10 nights instead for re-setting your earnings preference!