Wow - good build log. You are kind of doing in many ways almost the exact same build concept I am working with a Define XL R2 and this is my first go at serious case modification. I already removed the rivets on the 5.25 inch bay and now I have room for a 420 rad in the front and a 420 rad on top. I started with a grey/black Gigabyte mobo (X79-UP4) which looks just like the one you posted but now I'm looking at a Big Bang Xpower II since I have to RMA this Gigabyte board and I may not want to wait. I also bought metallic (I think it is tin but it looks like steel) sleeving for my PSU and fan wires and also for my tubing but I feel like it's too stiff and I need some color instead so I'll probably be using my purple and white mdpc sleeving. I also considered using a bay res + pump combo and bought the XSPC res/pump combo for the lang D5 since it's the only one that performs better than a regular D5 top according to martinsliquidlab but after testing it out I decided for a center-case mount for my pump would be better. I also hate the wiring and logos of my Seasonic Platnium 1000x PSU and want to mod it. I'm thinking I might use soundproofing material on it to give it a soft flat look? I didn't see this thread until just now but I've apparently been on the same path.
Anywho - I'm not sure what the cleanest way is to go about cutting the roof of the case to accommodate the 3x140mm and I could use some direction and you got mad skillz. I don't want to just slap a grill on the top and disrupt the clean continuity that drew me to Fractal Designs in the first place. Maybe mesh perforated aluminum that fits flush with the original case roof? I also might want to pick your brain about the aluminum front panel. I was originally thinking about using the existing mounts and simply creating a box around the entire thing but your solution is much more elegant.