This definitely helps. When going from the E to the A string I've been kind of palm muting the string which fixes it. I've been doing the Zimmerman book on the E and A strings, 1 - 1, 2 - 2, 4 - 4, slow. It's definitely an unorthodox approach but you gotta do what you gotta do sometimes. It won't be too long until my seasonal trip to my luthier so I will see what he says. Since this is a new bass and new fingerboard I think it will take a little bit to get it all dialed in. I think my preference for high action and low tension strings requires more scoop than the usual "modern" jazz set-up. This is definitely an issue that would only be noticeable in a studio.
The other thing I work on with my students is a slight overlap of sound on string crossings. In other words, don't release the first note until a microsecond after the next one starts to sound. It's not enough to be a true double stop and won't blur anything, but it does add to the sense of "articulated legato" in pizz playing and also tends to cover up the "clack" that sometimes happens when lifting the finger on a lower string.