As I have read various works that attempt to address the issue of anti-Judaism in the Gospel of John, it seems to me MOST scholars who have addressed this issue fail to make this distinction. As Dr. West noted in the previous post, there were many varieties of "Judaism" in the ancient world. Those who attempt to define "Judaism" narrowly, in my view, miss the point of the FG. In many ways, I see the "Jews" in the FG as something of a collective representative character; a character that is intended to represent adherents of those religious groups (other than "Christianity") that derive their core beliefs from interpretations/supplementations of the Torah. In my view, the Evangelist lumps these diverse groups under the rubric of the noun "Jew" and attempts to portray a Jesus who is the fulfillment of their messianic hopes.
How does this approach to the noun "Jews" impact the question of anti-Judaism in the FG? At the very least, I think it allows for something of a more positive expression of the Evangelist's anti-Judaic stance. This reading of the FG allows for the development of a historical Jesus who does NOT proclaim the inherent inferiority of Judaism. Instead, Jesus becomes something of a reformer/prophet who calls adherents of Judaism to return to the roots of their religious heritage (much like the OT prophets) and recognize the realization of the promises in the Torah in him.