Seems that your main limitations are space and time. How about packing the small chamber in the bottom with a media that has the largest surface area/volume for long-term bacterial colonization. How much flow is in there? Might be just right to allow for both nitrification and denitrification, if you get lucky

If really slow, a small pump in there should help.
In the short term, attach a container of some sort with a good amount of live rock to process ammonia, etc.). Over time, you can slowly remove the live rock and let the media take over nitrification duties. Denitrification