It's a simple 10 step plan!
Step 1) Buy Avon by QOTSA.
Step 2) Go to practice mode.
Step 3) Put a towel or something over your screen so you can only see the hit box (optionally, just try to ignore the rest of the screen).
Step 4) Play song by ear, watch notes explode.
Step 5) If the note passes the hitbox, add audio lag. If it doesn't reach the hitbox, lower it. Adjust till perfect.
Step 6) Slow the track down
Step 7) Mute the sound.
Step 8) Experiment with seeing how early or late you can hit a note.
Step 9) Adjust the video lag so you can hit as early as you can late
Step 10) Enjoy Guitar Hero!
Just so it's on topic, this is how I calibrated RB2 too, only I think I used The Middle instead of Avon. Any kind of auto-calibration, be it hardware or software, is bad.