The download might not of been loaded correct.
Stage 1 adds 2% more fuel and 2% more timing.
Exhaust has nothing to do with it.
Your cables might not be on the wheel correctly. Pull right hand cheese wedges and twist the throttle and see if the cable are tracking correct.
No need for motor to be running
Please add your state and model of bike you have. Click user CP @ top of page and then far left click edit signature. Thanks