I know i's a little different than you are setting up, but I just did a frag tank myself a few weeks ago. The same as you I have a TON of Capnella frags that I needed to make it for. The main differences are that I went with a bed of red sea pellets to stabilize the frags in instead of plexi or whatever, I am using LR rubble instead of plugs for bases, and I have mine cycling through my primary sump/fuge from the rest of my tanks (increased water volume, one stop maintenance).
Old pic:
Pic today (one month later):
It's grown in a little and become a SERIOUS pod breeder as well.
PS: I've never been a big fan of reef plugs of any kind. I don't buy corals on them, only rock. Why? It's completely unnatural looking in the DT to have this round plug sitting there as a base for a coral. It seems to me that the people who like plugs the most are fraggers (because they are easy).