A flashing SES light on obd2 means that the misfire is bad enough OR other problem is occuring that is bad enough, to cause damage to the emissions equipment. If you were close to me I would put my scanner on your car and tell you what its doing. Mine shows any current codes, pending codes, and shows live data with recording. Which with your situation sounds like what needs to be done with yours. Check your wires or go ahead and change them if its been a while and you have any doubts about them like the previous poster said. Also, like Injuneer said, check your cps. If you dont have the $ to replace stuff for "good measure" keep trying to find someone that will scan it. The more that light flashes, the more your raising your odds of replacing the cats and o2 sensors, plus whatever is causeing the problem to start with.... It could just be the tune too, like they said. You said it was crappy to start with so that may be enough to throw everything off and cause you more of a headache. What problems are you having getting your software to work?