As far as the 9V battery, the PC has to have power to set the 0 and 100 % throttle openings. If the engine is running, you can set the 0% at idle. However, if the engine is running, it will be screaming while you set the 100% setting. Therefore, in order to have power to the PC AND perform this calibration w/o the engine running, the PC needs the power from a 9V battery ONLY during this short calibration process. It doesn't stay connected.
You might see some gains at the top of the powerband. Most bikes run rich at high revs as a safety measure. Since the PC can take fuel away (negative values on a PC map) you can lean out the mixture on top to get a few more horsepower. I'm guessing maybe 2 or 3. Without a free-flowing exhaust AND intake, you'll still have the same bottleneck. The biggest gains will be in the low to mid-range where the stock fuel curve is lean.
"ride more, worry less"
2005 Suzuki GSXR1000 (slightly bent) - Track
2000 Honda VFR800 - Street