I bought new EMG pots for my Fender jazz bass(jap) and I was wondering why they are still scratchy sounding? I dont have any knobs on them at the time, is that the cause? Where can I get replacement knobs that would fit EMG pots?

id go to the place where i originally bought the bass and seek help there, if you ordered it, then i dont know

Only if you have a grounding problem. New pots shouldn't scratch.