Nate,
I have the Apogee Drive II and it has a pump on the top of the CPU cooler. IT is the HD with a pump the nozzel connections are on the memory sides but I do not think it will be an issue. If it is I will just get a new block. I Like the chipset block and I am really glad you decided to go with it. As for putting X79 Dark in red, I think it looks killer on my board, would it be an issue with the EVGA Bubbas to put EVGA by Natman_Doo on the chipset block in red same font at least for mine so it can be seen between the two 16X slots? My board hangs in my case the old fasioned way so the way you have it, through my case window it isn't upside down like the stupid back plates on the video cards.
Your CNC machine has really turned out to be one sweet setup. I looked at your photo bucket build. I will start like you said and try using the drill press with my milling bits. When I start working on the Mauser 98 I may ask for some advice.
V/R The Boatswain