You can do a break in with your new fuel setup. I'm just gonna copy and paste my break in procedure from my rebuild thread.
I wrote:Once you've put a few miles on the motor, take it out to a nice stretch of highway, preferably one with hills and get up to speed. Put the car in 4th gear at about 40 MPH. Then accellerate to about 60 MPH. Don't stomp on the gas, just gradually bring it up to 60. When you reach 60, let the car coast back to 40. Repeat this process about 5-10 times. This puts a varying load on the motor and helps the rings to seat in sooner. During my test drive, I could actually feel the motor gain more power as I did this.
The big thing with using an aftermarket fuel setup is to be sure you're running a hair rich so as not to run into a serious lean issue. You shouldn't be stressing the turbo to produce a ton of boost anyways, so I don't think you'll find yourself over taxing the fuel system, but a good base map, and not going pedal to the metal during the break in time will be just fine.
Also, don't forget to retorque the headgasket after 1,000 miles.