I am in the process of putting together a TJ08 build that is highly influenced by your great build. Quick couple of questions.
I really like how you used the gutted out fans. Why did you put them in the order that you did? That is, why did you put the gutted fan next to the ninja and not the noctua? Same questions applies to the front fan.
Also, can you completely remove the mb-tray with the ninja in place or just tilt it back like in the photos?
PS My build will be up on the gallery when completed
Very good question
Exhaust fan -- I didn't want a cantilevered fan because the rubber mounts have some play. Proximity of fan to HS doesn't give better airflow and perhaps more turbulence. Also I wanted the fan assembly to be easily serviceable without risk of damage to the fan or whacking the ninja (snapping the assy in/out of the case via rubber mounts requires some force in a tight space), and better access for cleaning with compressed air. Hope this makes sense, if not I have more photos.
Intake fan -- Here a cantilevered fan is the objective, it'd be pointless the other way around. I wanted to reduce the volume of compressible air inside the case, and move the fan away from the I/O panel on the front cover (per comments in Photo 13).
Last question -- Yes, mobo + ninja can be installed/removed as a complete assembly (per my comments in Photo 5).