while I'm not OK with what the shop charges, there is no doubt they are among the best in the business. Take it back and ask them to get it running properly. If the issue relates to their tune or any work they have done, it is their responsibility to fix at their cost.
Of course, if they convince you it was something else that would be at your cost.
And yes, PFC has always had a password option, and almost nobody uses it. I would discuss with them to have them remove it. A tune is just fuel and timing and there will be no magical intellectual property they have to protect, and of course if they say they are worried about you tuning it and blaming them they can use the built in tune compare tool to make sure your current tune is the same one it left the shop with; they will of course have kept a copy. It will cost you substantially more to take it to anyone else to tune from scratch if you need the tune tidied up for any reason.
One last point; there is absolutely nothing a tuner can do to increase response once the mechanical package is in place. They just get to choose how close to optimal power they make at each map point, weighing it against the risk of pinging and killing the engine.