Much of the tuning problems that I and others encountered came from people trying to be too clever and changing things that didn't need changing, or using advice of guys experienced on OBDI and earlier systems, or just changing too much stuff at one time and unable to isolate a problem.
To start off, make sure the PCV and crankcase ventilation system is set up correctly on a FI car. Here is a drawing Stazi made for CEG after we hammered out all the why/what-for questions that is pretty much the only Correct Way if you want to eliminate unknown influences while tuning.
See this image in the link below:
http://www.gtxr.net/turbo-vacuum-schematic.pdf
This is a schematic of the lines and how they should be hooked up. It's quick but accurate and easy enough to follow like a vacuum schematic.