Go to Travelocity to find published fares and classes by each airline. Manually work out all possible transfer combos, then run a search on the "Availability Tool" for all flights on that day one by one (i.e. if you want to go A-B and change at C or D, you look up all flts between A-C, C-B, A-D, D-B). If you manage to find the same (cheap) booking class on the same airline for every portion of your trip, you have a result! If not you will have to make do with what you got now which I don't think is too bad anyway.