I wouldn't bother trying to mod a Mac Pro. You'll be fighting against too many things- proprietary parts everywhere that were never designed to be modded, let alone removed. The heatsinks in a modern day (2009/2010/2012) Mac Pro aren't standard LGA heatsinks- the mounting pins are totally custom and the heatsinks carry fans and thermal sensors inside them. If you don't hook that stuff back up, the system will probably refuse to boot.
-SC
This idea just crossed my mind: Take the original heatsink, throw the cooler with the heatpipes inside out, take a regular CPU water block, make a custom plate with screw holes to fit the original holes, then take the stuff around the heatsink and place it in top, connect the temp sensors and stuff - shouldn't that work? You could use just the frame of the heatsink with the cables.
In terms of a radiator you probably will need to look for something external. I also thought about modding the sidedoor and make it a few inches wider to fit a rad in there, and then open it like a door with some flexible tubing in the corner. Hell lot of work.
Why not just do it in sections rather all out? cpu block, pump, hoses and a radiator for the cpu. Add more to your loop at a later date.
That is sexy!
http://www.million-dollar-pc.com/systems-2011/murderbox-mk2/murderbox-mk2.htm
In theory, I have the money to buy all that stuff. I'm just not sure whether I really want to spend such a hell lot of money.
I consider buying a Accelero Xtreme Plus II and just PCIe expansion fan that is completely silent, like a BeQuiet Silent Wing 2.
Can I change the fan inside the heatsink to get more airflow around the heatsink?