Too much sustain? Wow, never heard that as a complaint before. I've always found it easy to control sustain when I have plenty... it's the lack of sustain from an instrument when you want it is a bigger problem IME.
Well, to be honest, dropping the treble control, even all the way, should not be a problem. I've done it before and it still sounds great, so while that might not be something you're used to, it's not necessarily a problem to do so.
However, dropping all your mids and boosting the bass so much does seem odd. I'm assuming you're dropping mids from the high mid setting. May I suggest boosting the bass a little less and boosting the low mids a touch to help fortify the low end? Maybe also try favoring (or even soling) the neck pickup.
Also, strings are a big component too, and they'll do a LOT more than just change brilliance at the high end. Move to nickel strings first and see where that goes. The D'Addario XL's seem to be super common, easy to find, cheap, and a well known quantity in the bass world. Just make sure to get the extra long scale version for the 35" scale.
See where this takes you and report back.
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