Page 4-33 of the manual says "Don't disconnect couplers from ECM, battery cable from battery, ECM ground wire harness from engine or main fuse before confirming malfunction code (self-diagnostic trouble code) stored in memory. Such disconnection will erase memorized information in ECM memory."
Is it possible that you erased the code when you disconnected the battery and unplugged the ECU?
Give GoldenChild a call to walk you through it, and if doesn't give you a code (or gives you a "no malfunction" code), call Greg at Hyperbike.