For the vignetting, I assume you would only have to take a "master flat" for the lens/camera combination once and for all, and then keep re-use it (much like is done in DPP and DxO). Dust may move around of course. I was more interested in the pixel-to-pixel variation of the flat field - how flat is very flat? If you haven't measured it - no problem I can do it myself when opportunity presents, I was just curious if you already had the data. Same thing for the dark current static structure - how much is the pixel-to-pixel variation? I understand it's a differential measurement, but one should anyway be able to measure this (otherwise one couldn't calibrate for it).
0.05 electrons/pix/sec is great performance, 1 electron/pix/sec not so much. The dark current seems to be (surprisingly) temperature sensitive in this regime. That means one needs to match the temperature of the sensor fairly accurately for the dark. Alternatively, optimise the dark subtraction by scaling it with the help of a bias frame.
The 5D2 sensor is also famous for some "band" structure in the dark that unfortunately is not stable in between exposures, and so very difficult to properly remove. Have you made any progress in this area? It will be interesting to see if the 60Da improves in this area.