I would get a refurb now that they seem to have it, if you're on a lower budget. 6-core is nice, 8 would be better, but if I had the choice I would get D700 before upgrading to 8 core. You can upgrade RAM later, but if you're spending this amount I would go for 32 GB. Also, I would rather go D700 and live with 256 SSD if you had to make a choice.
That 2009 is getting long in the tooth, and you won't have Thunderbolt. Not a bad machine, though.
I agree with Ben B. What is your future aspirations? If you know your going to be doing 4K RAW and beyond then build for that.
Just an FYI, I recently built a machine similar to that older Mac Pro. It can handle 4K but it isn't as fluid as a modern day Intel chipset(like a new Mac Pro, iMac, etc...).