Mash, if it's not too much trouble could you link to the PCI Extenders you are using? Are they pretty much like these:
http://www.amazon.com/gp/product/B002M1DHJG?tag=at055-20I haven't used extenders before but think I will try them out.
Zxy-=> 1200w is overkill for 2 cards IMHO. Two cards can run on quality 750W psu. 1200w would be more suitable for 3 cards.
I'd also recommend just building a 2 card system first instead of a 3 card one. You'll have the ability to go to 3 cards but it'll much easier to put the 2 card machine together at first.
For GPU's I would not go with the 5000 series unless you found a really good deal on used cards. For price to performance you'll want to go with newer generations.
I'd also recommend sticking with video cards of the same series. As you are just starting out, it will be easier to determine any problems, and see your performance levels, if you are using the same cards. It just gets a bit more complicated if you are using a mix-and-match.