I have rented the CF-39 back and H2 Camera for a week shoot recently, and also been using Phase one back regularly (from H5 to P25) and on a couple occasion a Leaf. I'll just give you my general opinion and feel of the system
The integration Camera/Back is great, the best among MF backs perhaps. But battery draw can be pretty quick, especially if using the CR123A adapter, maybe just one or two hours of shooting. The screen at the back is decent, but lack of certain clarity for focus check, and could be a bit slow (couple of big seconds.. ) to zoom in for focus checking. Mind you I mostly have used the back in non very friendly conditions (very warm weather 30 to 38 C, extreme dust, night, very little time to set-up.. etc..) and on a couple of occasion, it will hang, and you need to take out the viewfinder of the H2 camera, to access the button needed to release the back from the camera, put it back on, and re-power the whole thing...
Also the backs in my experience runs very hot... and with the fan spinning all the time, i dont' know how hots it runs at room temperature because we always used it on location, but by guess it was around 50 C at times.
Regarding the Flexcolor and the pixels, I'm pretty happy with the quality of the files expect at times it gives a slight Pattern/ moire in the shadow area that can be pretty visible. Also the overexposition of the skin creates magenta and blue pixels, similar to the feel of the Kodak DCS Pro SLR which didn't have the anti alias filter, it a sort of moire i presume, but i'm not entirely sure. It seems to be of one the side of too much details and color noise. the files are rarely "clean"
Also Flex Color isn't as straight forward to use as Capture for me. I find the workflow in capture one better, but that's also a question of choice. The software needs a pretty beffy laptop to shoot on as one could imagine. The ranking and selecting system isn't very intuitive. No way to have side by side, but do all kinds button pushing and menu digging to apply color settings to a batch.
But apart from that, it is a nice combo, and the H2+CF39 works quite interestingly together, feels more integrated than other combo, and has a good feel in hand.
Hope this is helpfull. I have some crops if you need.
Cheers..