Does it have an immobilizer or starter interlock? I don't know much about modern motorcycle security systems but it's a possibility if it follows standard automotive practice. If the battery dies it may need to be initialized somehow. Does the starter even operate normally with a fresh battery? The battery is the heart of any charging system and if it's dead flat, a jump might not be able to overcome that void. You've verified a lack of fuel or spark under cranking? What does it use as a trigger for injection and spark? You've got to confirm fuel pressure, then make sure the ECU is receiving proper inputs before condemning it. It's never good to "let the smoke out", though, because everyone knows that electrical systems operate on smoke transfer, and when it comes out they stop working. Good luck!