My issue with drilling is knowing if we have tempered glass or not, how do you know? Otherwise wouldn't be an issue and would work great, save lots of time.
As for filter media we are going to do half and half ceramic rings on the up flow in the sump and srubbies on the down flow in them baffles(there are 4 chambers) Under the ceramic rings we will put a 36" air wand! I want to eventually swap scrubbies for pond matrix. I had considered putting air wands on the down flow but thought they might make things goofy, I'll experiment bur right now two wands in the two upflow baffle chambers.
Sounds like a very good design. I like the bubble wands under the ceramic media... that should be a big boost the the bacterial colony. Having submerged ceramic media should also sustain the bacterial colony longer during a power outage than an air based colony... (I have nothing to back that up but it sound logical).
I like the gas exchange surface area sumps provide.... It sounds like you should have plenty with your implementation.