Just about everyone that adds a header is going to have some low end response issues. Those being idle hunt and low rpm stumble/flat spot to some degree. The best way to deal with it is to have the bike mapped correctly and the pilot jet mod. The map is a bike by bike issue and the pilot jet mod helps all modified bikes. It will never run as good as stock on the low end, that is the sacrifice you make for high RPM horses. But you can minimize it to the extent where its hardly noticeable. The jet mod will smooth it out considerably and helps with the idle some too. This link should explain everything about how to do the pilot jet mod: pub56.ezboard.com/fkawasakizx12rfrm1.showMessage?topicID=6026.topic
I have a full Yosh header, K&N's, Yosh EMS, timing advanced +3 to +4 degrees, pilot jet mod, and the bike runs very smooth at low RPMs. It still has a bit of idle hunt when its cold but that goes away as soon as the bike warms up.
Advancing the timing about +4 seems to give real good results and is still resonably conservative enough to where you aren't going to have any problems as long as you run super unleaded. Gives the bike a different feel. Makes it rev more like a dirt bike.