Mmmmhhhh, I just set up my new Stingray with that setup you mentioned (E highest.....). Take a look at your fretboard. Is it straight or has a "radius", so to say a "round" surface. If its round you might want to set up the string high in relation to the "radius". E and G quite the same hight and A and D a bit higher. (My explanations sucks, but hey it not my mother language

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Sadly my Stingray has a round fingerboard but if I lower my E-String as I just told it buzzes

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So if you dont like it as it is. Change it.
I would recommend that you first try that new setup a bit. Two things can happen.1. The feel comes with time. 2.You get really annoyed by it.

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