It sounds like you're running lean at idle/low rpms. If you don't have an AFC you can make the smaller hole in the orrifice for the jwt low driveability hose. This will trick the ecu into make the mixture a little rich at idle. You can test this by pinching the new hose that is going to the dual pop. If it makes the idle smoother you need to richen it by making the orrifice(spelling?) smaller.
The new HKS fuel controller has a separate idle adjustment that the Apexi AFC doesn't. You might want to consider that too. With my AFC I could make it run just right witht those 720cc injectors but then the O2 sensors would start leaning it out again.