okay....coupla off the wall thoughts
you want to block that hole, and drill yet another much higher up, where you want the surface of the water to be.
couldnt he get away w/ a stand pipe/riser from the left side/ entry toward the sand bed? Not really worried about leakage since its in a wet environment....
Is this gonna be a reef? I'm guessing so since you want to add a refugium...other wise you've got plans for one monster mandarin tank!
If you have the room/space to dedicate to this, I think that the simplest way of doing this would be to seal the three holes on the compart on the right's, right side. (lose any one yet?) I would close them off/ turn them into ball valves or Union ball valves, with the main idea behind them being flexbility for the future. you want to add a chiller...no problem, ya got the access, no need to buy a drop in model. Want to run a calcium reactor??? same thing...how about your fresh water RO/DI topoff???? Plumb another tank into the sump??? possibilities are endless...
I would remove all the bio media, brace the bottom of the bio media compartment (egg crate) w/ something, and stick a bunch of rock in there. Adding the stand pipe like I suggested earlier will raise the water level in the sump, which will cover the rocks I'm suggesting you put in the sump. You want the rocks underwater to provide anaerobic, (no oxygen...home to nitrate eating bacteria) zones deep w/in the rock. Otherwise you'll wind up w/ more aerobic bacteria, (has oxygen...bacteria here produce nitrate....this is the same bacteria that will live on the bio media we are trying so hard to get you to ditch).
remember to allow for room for back siphoned water in the sump! If you have a power shortage and the standpipe is too high, all that extra water will be on your floor.
The now largely empty second compartment, (right side w/ all the holes in it) could be used to hold your heater, skimmer, etc, and act as a settling tank for detritus...
Finally, I would use the last remaining ball valve/union ball valve/ hole to connect to a pump running to a seperate refugium. This way you are using this sump, and you arent modifying it beyond its useful capabilities. I think you can pick up a rubbermaid stock container fairly inexpensively. I believe Reef Lady is using one of those for her refugium.
if this is possible for you, I would consider it.
I've seen Jesse James on Monster Garage turn a 5.0 mustang into a 100 mph lawn mower...but if I really want a lawn mower I'm probably gonna go to Sears and buy one that works like I need it to, as opposed to spending lots of time and money converting my car into one that will almost do what I want....
(never did figure out where they hooked up the grass catcher to that thing?????)
Hope this helps...
Nick