Mate,I think that exhaust place is full of it.But play their game and give it a few days,then if its no better,take it back to them and tell them you want it fixed..Ive never had a problem with a car running like crap because an aftermarket exhaust system was fitted.And Ive helped mates fit a few of them, and I have done a few myself.And what has happened to your car, has not happened to any that Ive done,so theres something not right there somewhere..And as for the computer,it will adjust itself pretty much straight away after the engine is started .The fuel trims might take a bit of time to work themselves out,but they wont cause it to hunt and run bad etc.Id say the exhaust place has probably knocked something off around the engine somewhere and they havent realised,like a vacuum hose at the rear of the engine or whatever.