@Valantar thanks!
For tubing I'm already using 6/10mm (1/4" x 3/8"), going smaller would be possible but like you said, I already have fittings. Plus 6/10 is already fairly small.
For the alignment of the rad/ mobo, your eyes aren't playing tricks on you. Since I'm using my first draft of the spine plate the radiator is 1cm or so higher than it needs to be relative to the mobo. I've since corrected it, but not had a chance to print the whole spine with corrected placements. Hopefully I can do that this week, though. I'm not 100% sure if the pump will fit under the mobo tray with the psu in place, but once I have he new spine printed we'll find out. If it does, that's wonderful, but right now I'm thinking it's going to end up on it's side near the mobo or in front of the rad like I said.