I took some time today at the Fablab to learn about the water jet cutter. I was lucky enough to catch Manny cutting a piece of 1/2" plexi and he graciously allowed my to watch and ask questions. The main question was "will it cut wood?" Hardwood should work so that makes cutting the slot in my block base simple (as long as it works well). I also talked to Scott for some help with the CNC component of my design. Some issues that came up were depth of cut, bit size, and material literally lighting on fire. Good think I have plenty of wood mess with.
With all the computer work finished, the rest of this process (cutting and assembly) should go rather smoothly. With my extra material I'm going to create a smaller version of the project to make ensure minimal difficulty when machining the final product.
Here's an exciting GIF of the water jet cutting 1/2" plexi for a 3D printer enclosure.