Dakyn - if the AP was unable to initialize the ECU then I imagine you may run into another road block when you go to have the car tuned. Be sure to alert your tuner ahead of time too.
Smoke Test = you need to find a shop with a smoke machine.
Wastegate = try lengthening the rod by 1 full turn (counter clock wise). See if that helps.
Stephen
www.facebook.com/iaperformance