I had a similar experience, although not as much has been done to my car. Oil contaminated MAF, had to ditch the power duct and ported throttle body a dealer sold me (also sold me the BlackWing and I let them install it...reason for oil contaminated MAF). During the header install, I boogered a pigtail connector to the #5 injector, and broke the #7 spark plug. JR was able to point them all out, and get the tune done. Sooooo niiiiiicce!
I can't wait to get the WI on the car and get it re-tuned!