I apologize if you already knew this, but..
The PFC must learn the idle of the car once you first install the unit.
What I did was initialize the PFC, configure the injector correction (for bigger injectors), then follow the idle learn process that can be found on the paulr33 site.. if you dont have the boost control kit,make sure thats turned off in the etc menu.
Also, it helps to verify your aac valve is clean and operational.
I would advise against changing the timing to accomodate the idle as said before, youre making temporary changes to the entire map.
After my self-learn process, my car idled at a solid 700rpm. A little low, but fine tuned with the adjustment screw from there, which is also a process, not simply turning the screw.
Keep in mind, if theres already a tune saved to the unit, you will lose all of that data by initializing the unit. It will take you back to the japanese base map for a completely stock setup.