I have used SD TWRP to flash CM, but how do I get 2.6.3.1? It is not automatically flashed in GooManager...
It's now a moot point as your issue is solved, but you could make a flashable zip for any recovery .img using info at the link I referenced above (http://xdaforums.com/showpost.php?p=49111924&postcount=8).There is no zip for 2.6.3.1, but I found an app that flashes the recovery for me; this issue is solved.