You could try any number of things. A different pulley would work to bring your boost down too.
Ultimately, you're just watching your AFRs to see if they are in the ballpark of where they used to be. If they're higher (leaner), you're ECU is probably pulling timing, and you should change the tables to fuel for it. That way, you get the proper fuel and all of your timing.
Think of it this way: air, fuel, spark. If you have a good tune, then the three components are working in harmony, and you're making power safely. If you change one of those three components, the other components need to compensate.
In this case, you changed the air component. ...and possibly fuel quality, but we'll ignore that for now. If you give it more air, you'll need to give it more fuel. The ECU might do that for you, AFR's will tell you if it is. If not, you'll need to get in there and change the tables. If the ECU can't adjust to the fuel demand, it will pull timing (the spark component). If you're running more air with the same fuel, this is most likely what's happening. You don't want to be in this scenario. Pulling timing is the ECU's way of keeping your motor safe. If you're normally running around with your timing pulled, then you're decreasing the threshold of *how much more* timing the ECU can pull. In other words, you're getting closer to running out of the protection that the ECU can do for you.
All of this is playing within the boundaries of what the ECU allows. If you get to the edge of what it allows, you'll get a light, and go in to limp mode. Or you will det, the ECU won't catch it, and you'll hurt your motor. This is a possibility in the lower gears where the RPM's sweep through the rev range very quickly.
But back to basics: air, fuel, spark. You can change one and compensate, or you can change your setup to bring the air component back to where it was when you were tuned. That's what you were asking about with the stock exhaust. If you're going this route, I'd say it would be better to change pulleys back to the PSI you were tuned for, and keep the rest of the car as it was. Hope this helps!
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