Solution:
Extend the cord for fan, and run it up another location.
Thanks for posting your solution, this is what I ended up doing as well. I've been busy with work and haven't had a chance to post pictures, so thanks for sharing yours!

Solution:
Extend the cord for fan, and run it up another location.
Originally i had bought and installed a Zalman vf-900cu, but STAY AWAY FROM THIS COOLER! It includes thumbscrews to hold the cooler in place, and they stick out a long way from the back of the card.
It might be a good alternative for a PC that has lots of space inside the case, but since the mac pro only has a few millimeters of space between the case and the back of the ATI card it would not fit in the bottom PCIe slot.
I hat to move my card to the second slot, forcing me to run it at 8x, and i was about to give up and just live with that until i saw this thread.
I ordered an AT1, and it arrived today. What a great cooler!
I had a huge problem though, the Zalman has separate ram heatsinks that you glue on, and i read about many people who ruined their cards trying to get them off again. I'm happy to say my card was undamaged after 15 minutes of painful twisting and tugging on those things. Using a sharp knife helped!
As for those of you complaining about the power cable - you already voided your cards warranty by replacing the stock cooler so why not take the time to cut the molex connector off your AT1 and cut the original connector off the stock fan, then splicing it together. Even if you don't have a soldering iron, you can twist them together and use tape or hot glue (or both!) to make sure it is insulated and staying together. (i would recommend buying a soldering iron though, those are really useful. just read a soldering tutorial online to get started...)
Connect red to red, black to black and leave the white one unconnected. That's all there's to it.
So now i have a dead silent card, that will automatically ramp up the fan speed if things get hot. Perfect!
other round of photos.