If the issues STARTED when you installed the QS3 , that is where I would look ..... you need to adjust it according to the instructions , that is the leak jet screw on the side , and if it is not correct , you will have issues ..... A buddy of mine put one on his 2011 KTM 450SXF , and he ended up killing the battery trying to start it , and keep it running .... I looked at the instructions , checked the setting , and it was way off , I adjusted it to what the instructions said and the bike fired right up , it was still temperamental , but better .... personally I prefer the QS2 , it does not have the adjustable Leak Jet , and it works so much better ....
The main purpose of the QS pump covers is to give you more gas volume in the AP , the Leak Jet add on , to me is too much for minimal benefit and more adjusting needed to be done ... basically its Snake Oil for your carb , you are better off just buying the correct size leak jet and forget the adjustable one , there is really no need for it , all it does is regulate the BY-Pass fuel that the AP does not use in the squirt ... but it makes tuning a nightmare as far as I am concerned ...................