If you just wan't to get rid of the check engine light then all you have to do is run stage 2 or stage 2+.
As far as logging: Select what channels you want to log. I do RPM, throttle position, timing cyl 1-6(you PROcede guys don't know nothing bout that
), charge air temp, lambda 1&2, WGDC, load req&act, and boost.
Then find a safe, empty stretch of highway and do either a 2-3 gear pull or 3-4 gear. I do 2-3 because of safety reasons.
Select monitor->datalog and start logging right before you go WOT.
Then hook up the AP to your PC and export the files. Use excel or virtual dyno to graph the logs and post em to get some reviews.
Ohh, and I've got nearly 20K miles of trouble free EXCELLENT performance from Cobb.