My guess (and let me emphasise that's just what it is) there's going to be two versions.
1. Something with a single CPU. I don't think they'll bother with E3's. They will possibly use the not yer released E5 1XXX series. Single CPU, not expandable. With half decent graphics and the new design they can MAYBE get it out the door a little over 3K. Remember, every board in there is custom, so they won't be able to cut corners by using derivatives of mass produced Intel boards and the associated volume production savings.
Twelve cores on a single socket means Xeon E5's v2, aka Ivy Bridge-E. This was confirmed the day of the new Mac Pro revealed.
Other recent benchmark leaks point toward a 6 core model as well.
2. Then, for those who are so inclined, a 2 CPU solution. This is NOT a server box, and currently the only muscle workstation CPU is the 2687W. This is a 2K part. For ONE CPU. So imagine a 2 CPU box (OK, keg) with something like a Quadro 6000 equivalent. That's a 3.5K graphics card in it's standard form, how much a design they'll be able to shoehorn into that keg is going to cost is anyone's guess.
Except Apple announced the new Mac Pro with its standard configuration containing
two FirePro W9000 cards that cost ~$3300 USD.
As far as thermals go, the CPU is rated for 130W max, the GPU's are 275W max so the shared heat sink/fan has to deal with 680W under full load without having to throttle due to thermals.
There is a problem with Apple offering a 2 CPU version: there isn't physically enough room. The secondary CPU board would have to occupy the space that one of the GPU's do in the released pictures. The cooling system is an isosceles triangle too: the equal length sides support the two GPU's.
So you are talking 7.5K USD retail for the CPU and graphics card, excluding everything else and Apple tax. How much is this going to cost with filled memory banks? 12K ? 15 ?
The memory expense shouldn't be that much. I picked up 128 GB of registered ECC 1.35v 1600 Mhz DDR3 memory for a workstation at home for just under $1k USD earlier this year. For Apple, getting 64 GB at 1866 Mhz speed should be under $500 USD. The downside is that going with 128 GB of RAM would require the usage of 32 GB DIMM's which go for 2.5x to 3x the cost of 16 GB DIMM's. Those looking to upgrade from 64 GB will also have to remove all their memory and replace with higher capacity models.
There is a bit more than just the CPU's, GPU's and memory. There are Intel C600 series chipset, three Thunderbolt controllers, the SATA-Express controllers, USB 3 controllers (these are not part of the Intel chipset), case and power supply.
The one thing Apple has going for it is OEM pricing which can be radically less than retail pricing. Even then, I'd be surprised if this new box was less than $6k USD at launch with the two FirePro GPU's and six core Ivy Bridge-E chip.