Hi Scott,
I'm showing my age here, but my experience with motors goes back to the early 70's. Not that I'm a great mechanic or anything, I've just tinkered with cars & bikes a good deal.
As long as you use some of the tuned maps that are available with UTEC's you'll not likely damage your motor. In fact the Turbo XS and Vishnu units will likely make your car run MORE efficiently. It isn't unusual for stock mapping to be overly lean in order to pass stringent smog regs. As a result those lean settings can cause problems. Going to aftermarket computers gives you outstanding tunability with some excellent electronic automatic control to protect your engine from detonation or excessive boost conditions. You also can pass all the tailpipe tests by simply switching to the stock map
The Turbo XS unit is due here today, so after I teach tonight, I may hook it up. I'll start a new thread with details.