You're overcorrecting.
First off, your fastest way to solve these issues is to take the thing to someone with years of experience on a wide range of basses.
If you want to experiment yourself, then you need to take detailed notes. I think the first place you need to start is to learn how to adjust soundpost position (this is what luthiers do, not skating the bridge all over the top of the bass) and put the bridge in the standard position and keep your cotton-pickin' hands off it.
From what I have read and heard, you're doing the analogue to trying to fix an ignition problem by rebuilding the carburetor.
Ok, I think Chris and a few other guys I think have the situation down.
It's the strings and sound post problems.
I use special solo strings and they are lower to the fingerboard, so absolutely It is something on those lines.
I also agree it's the crap pickup as well.
I don't notice as much when I use the Ischell but I have to find the perfect spot if I use the Ischell again on a new bass.