1. What are the cal / alk / mag sections in the front? I'd think that is where you'd want your scrubber so you can look at the growth.
2. The design looks good; I'd use sliced airline for the bubbler.
3. The LEDs seem too much. 3 cubes only needs a minimum total of 36 CFL watts, or 12 LED watts, or double that for a maximum. I'd just do 12 LED watts, which would be four 3-watt LEDs. See how this unit started growing with just two LEDs:
https://www.youtube.com/watch?v=91jQAPB40OA
4. GAC carbon is fine; will not affect scrubber. It only removes DOCs, which unfortunately includes coral foods such as Vitamin C, etc.