The iinstructions that came with mine state "9. Start the motorcycle......If the green and red LEDS continue flashing after startup please refer to ...[trouble shooting guide] or call tech support...." Perhaps not so much misleading but it appears you may have gone straight to the Troubleshoot section. That's what happens when we try to do the right thing and read the instructions.
It really is a simple install and I'm thrilled with it; only a slight increase in fuel consumption (largely due to the way I'm pushing it), no decel popping at all, very smooth take up and a lot more grunt. Hope you can sort it out and Im sure you'll be similarly pleased.