Probably has nothing to do with the turbo or the kit itself. Look for vacuum leaks to start, ensure all your electronics are properly plugged in. Are you running the stock MAF or did you change it? Is all of the air going through the MAF, or is the intake tubing letting air in somewhere? What else changed with the turbo kit?
There are a lot of reasons that might cause an engine to run rough. You need someone who can diagnose it by listening and looking at what's going on. I mean, you basically told us, "my car is running rough. Why?"