Yeah, the first thing that you need to do is find out what the ECU is b****ing about before getting over stressed about potential causes. I just installed a Reband on my 13 R3T which promptly threw a P0130 oxygen sensor code during the 12 minute tune after loading a updated tune in it. Said WTF, cleared it and went riding. The bike ran fine and 400 miles later the CEL still hasn't returned. I attribute it to the new pipe and sealant on the collector out gassing and causing the O2S to not return the data that the ECU was looking to see.
If your code reader supports data stream display that will be helpful if the code resets. Probably want to get TuneEcu anyway though. It isn't up to the level of Tune Boy but for 29 bux (what I paid for the cable) it is hard to beat for the money. Besides that you are probably going to have to load a new tune in to her anyway. Unless there is a tuner near to you that can do a custom map for you.