I assume the OP wasn't interested in the classic Mac Pro. I've considered the 5,1 as well but unfortunately, it is short one hard drive for me...if I were going to go with a 5,1 I would need 6 3.5" HDDs (I can run the SSD RAID array via PCI-E 2.0 expansion but I'd want the HDDs internally. Oh well. The issue of TB2 doesn't matter since you have PCI-E 2.0. I guess when you upgrade to the Titan GPU, running 1 or 2 4ks isn't an issue? Has anybody run more than 2 4ks?
I'm curious how much that setup cost you, sans storage. And have you had any difficulties upgrading OS X beyond needing to flash firmware (and why do you have to do that)? Did you upgrade your PSU? What PSU comes with the 4,1 and 5,1?
Oh my bad, I obviously didn't understand that at all. Yes, you are absolutely right when it comes to the 6,1.
You could mount six 3.5" HDDs internally, but only if you are willing to use the optical bays.
Yes, MacVidCards has run at least three 4K displays, maybe more.
The firmware flash isn't related to OS X upgrades. The firmware flash upgrades a 4,1 into a 5,1 with the main point being that Westmere CPUs are enabled. It basically takes the Apple official 5,1 firmware update file (that you download yourself) and applies it to the non-approved but totally compatible 4,1. There are some other minor side benefits too.
The PSUs cannot be upgraded but do not need to be. I think it is 950 watts or something. There are people running 12 cores, 8 sticks of RAM, and dual GTX 970 video cards.
I'm not really sure what it cost me. I bought the 5,1 new (refurb) in 2010 and slowly added upgrades over time.
Looking at Ebay, you can get a basic single core 4,1 for about $450. Firmware flash free. RAM is fairly cheap. The CPU will run $200 for the top of the line 3.46GHz hexacore (W3690) or $70 for the quadcore equivalent (x5677). CPU price falls
very fast for each step down in speed (seriously a W3680 is only 130MHz slower but $40 cheaper). GPU depends, but GTX 680 minimum for 4K, and all the way up to Titan X. USB 3.0 about $30-$170.
It will never have Thunderbolt though.
If you want to know more, it's best to ask in the Mac Pro forum. My knowledge is limited.