I would definitely speak to an authorized dealer of whatever digital back platform of choice is. Once you engage one of these guys (the reputible ones) they will help you decide and work up a package for you. I know for a fact that they can beat the price with a Mamiya 645AFD system and P45+ 3 year for the price of teh H3d, and for 3k more you can get the system with a 3yr warranty and a one year swapout priveledge. So when the 'next' camera platform ships, you can swap at n/c .
You can even do better with a P30+ bundle from a dealer that will be closer to the H3d31.
Also look into the bigger picture as well, workflow. How do you plan to process your RAWS, is it important to you that PhaseOne has developed and set the bar for RAW processing that if you are moving up from a DSLR , you can use one application for all your files. Sure there is lightroom out there now as well, but I believe that if a company develops software for thier back most likely that will yeild the best results for that hardware. As we have seen in previous posts, there are some manufactures who can still not produce consistent stable releases of thier own software (multi-platform), so how if they cannot get it totally right expect a third party to do it correctly?
Next think about modularity and openness. Do you want to be totally locked into one platform with no option to ever change? A Hasselblad 553elx/d could have been used since the first Leaf DCB and still used today with the latest and greatest digital back out there. Come one look at the chatter about Contax. It may not be made anymore, but they still work and are solid. It is crazy how I hear people going backward in technology on their camera platform, but are buying the latest digital; back.
Another question that comes to mind is why it costs more for you to purchase a CF39 and H2 system, than it does to purchase the same hardware that is a closed system from the same manufacture. Oh,but wait there is more.....You get a FREE lens of your choice(not verifed, saw post above) if you purchase the 'closed' or 'integrated' system? So look at Hasselblads prices of a back with a one year warranty that is not integrated into their camera system, the prices are right up there with Phase!
So why are they so interested in selling the integrated system at what probably is a lose? Do they not have confidence in their digital back on its own? Can they only make it look good if they do software magic themselves?
Anyway sorry if this was long but it gets frustrating seeing people go through all of this, when if upfront they contact a reputable reseller (there have been a few mentioned here) and engage them in open conversations about this, you can most likely get additional info. These guys have dealt with a broad range of users, and most likely have answered the questions you are asking many times.
Also try it out for yourself, there is not one system that will fit all needs.