Good question, The most important mod is keeping the shrimp out of the back. To do this, I plugged up the lower vents with some filter floss, you could also super glue a sheet of plastic over it, from the front side or the back, or glue some mesh screening, or stainless steel mesh over it. Then, I had a stainless steel filter intake screen, that was probably 1.5" in diameter and ~7" tall, I cut it open down one side and across the bottom then butterflied the thing open. I tried using superglue gel and hot glue to attach this over the upper vent slots, I found the hot glue works best, Just make sure you get this on good because if it busts loose later on it's a pain to fix! If you can manage this you get an awesome shrimp tank!
Other mods, I grew some emersed plants in the back chambers. That living basil you can get at the grocery store does really well with it's roots wet (might have to find a creative planter to keep it in, or a pot just larger up top than a chamber), but keep the stems above water. It will send down extensive roots, which will help keep the water clean.
Also-you may want to go open top with a custom light such as LED if the temps are running hot. With that enclosed lid and all that PC lighting, it can generate a lot of heat and keep it in. Just set it up and keep an eye on it for a few days.
I had the same problem with my planted biocube 14. I can't even get my hand down chamber 1 to plug the lower vent. I'd rather not block from the front due to ascetics. It's very much a pain!
It's nice to see another Biocube owner posting a planted tank!