Shame to see the Minja go, was a tough little cooler with plenty of heatpipe power. Excellent for low airflow.
Smallest they've now got by fan size is the ZZ already mentioned, which got excellent marks on the previous test platform for both high and low airflow
. The snag here is that it's a top-down cooler, so sideways airflow may be less than ideal. Better than the Big Shuriken, but might still not be enough for comfort.
I think today you'll be left looking at small tower coolers. Unfortunately everywhere I looked (Nexus, Thermalright, Zalman, Noctua, Xigmatek) it was all tight-finned, ergo poor for low airflow (low pressure) scenarios. If you find one that fits, however, and can duct it to the case fan without compromising VRM cooling (two fans should mean no problem), I think that might be your best bet for efficient cooling.
If you have an extremely low-power setup, however, you might be able to get away with it without ducting. The only way to know is to try, or find someone else who has.
PS. I know it's a long shot, but some of the "single-unit" water coolers available today are relatively decent. If you're really pressed for cooling power, they could be an option, since you have the 120 mm fan openings required. Might take some doing with the protruding grills though.