Wow some great tips here, great job fretless guys!!! You're describing stuff that I do and don't even think about.
I love having a fretless with two humbucking pickups. I'm not a big "mwah" guy, I like the electric fretless 'plunk' that Sting used to get with the Police. As such, I use flatwound strings and tend to favor the neck pickup.
However, even on my bass with flats, if I favor the bridge pickup and move my plucking hand towards the neck, even over the neck, I can get a nice midrangy fretless singing tone. Not quite the roundwound "mwah", but a nice singing tone. It sounds extraordinary with chords, and my intonation with chords is actually not that terrible.
BTW, If I were you I would change the pickup blend to favor the bridge pickup before I started making EQ setting changes. My bass has a passive EQ and I find that the change of pickups makes a very dramatic difference towards the midrangy mwah and it's more "natural" sounding than just boosting EQ would be. Low action is nice, I like relatively middlin' action on my basses, but lower action on the 6 string fretless helps a lot with chords.
It may be worth a look in the "technique" and "setup" forums for more information, this subject spans basses, technique, and setup.
BTW, Nice bass!!!!!
