Hupmunk accepts a (very very limited) subset of the advanced commands from matrix. Perhaps you can try searching there using your connecting cities (and the the airline filter on the results page).

If you're familiar with userscripts you can also use this to try and get direct links to orbitz/hipmunk/priceline etc. (you could also try Delta, but I doubt it will price into the deep discount economy fares). It doesn't always price correctly, but worth a try.