I love the stock look, but I wouldn't (personally) go to extreme lengths to make it look completely stock.
The FMIC would give it away anyway so just rock the full 3" turbo back exhaust too. There are enough variables in getting these cars running right and reliably without dealing with electronic cutouts and rerouted pipes and everything.
And "somewhat stock" will keep the ricer wannabes away too. I have had several guys rev on me in my car only to see the FMIC and Exhaust and gauges and immediately back off. It helps to prevent asshats from wasting your time.