I'm on my second Hasselblad body and back (first had an H3DII-39, now an H5D50), and I've been very happy with the decision. The lens line-up and color are great (I use Phocus). As are True Focus, 1/800 syncing, large viewfinder, ergonomics, tethering into Phocus, etc. I think the depth of the files will amaze you, especially coming from the 5D Mark II (which I also have).
As for your decision, I'm pretty sure the H3D-39 has a larger sensor than the P40+. It's also a terrific sensor, even if it's not the latest generation. Remember, at the time it was one of the top sensors in the world, and it's performing now just as well as it did then. My H3DII-39 had the same sensor, and I loved it. I think the pluses of the P40+, if you need them, are a higher base ISO and a higher top ISO.