plus there's no direct evidence of the use of any specifically Qumran texts that one would expect to find if there was a direct link.
True, I certainly don't dispute that but this too cannot be used as evidence of a lack of direct influence from the Qumran texts upon John, as there are many reasons why someone might not want to directly quote a non-scriptural text as an authority (i.e. its not considered 'divinely inspired' for a start, so will it convince the reader if cited in an argument?).
I think Charlesworth and co. have a strong point, inasmuch as John and the Qumranite author both use the light/dark dualism to mean the same things ("life, truth, knowledge, eternal life"), in a manner that is not reflected in usage of this duality in other Second Temple texts that exhibit it (and also how both 'qualify' their dualism in the same way). When pared with the same or substantially similar terminology, I personally think its evident that appeal to a 'general' Second Temple Jewish background (whilst accurate in the broadstrokes) doesn't really account for these shared 'details' (which are more specific and seem to hint at influence).
But, who knows? There was certainly something in the "ether" during the Second Temple period anyway that many different Jewish sects imbibed as part of a shared overarching intellectual culture.
So, I agree with you on previous sources/ideas in the Second Temple era influencing both groups even in the absence of direct influence from one to the other.
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