Nice catch, the 1st gen are notorious for leaks at the wastegate. And YES, there is a thin gasket which is no longer available to purchase. This gasket will detiorate over time and S/C rebuilders use RTV to remedy this gasket issue. From the info provided, your ECU should be stock. As suggested, once you remove the S/C and disconnect the battery during that process. When you reconnect the battery the ECU will reset itself over a few hundred miles to accept is new setup. NO BIGGIE.
FYI, more than likely you do have colder plugs try pulling a plug to verify. Further, you should be running premiun gas as well. Another notorious issue is pinging, a leaning issue. Best described as a bunch of marble tossed around in a can sound.
If it's pinging and you don't want fuel mods, try the " anti-ping pulley" if you can find one. I have one and it worked great when I used it.
However, from those of us with S/C envy and you do too you just don't know it yet, LOL. What you will notice is how much you will miss the S/C performance. Drive a stock 3.4L before you pull the S/C. That should help with your decision.
Regards.........8sm