Well, instead of waiting for other dialog, I went for it.
I have good news and bad news. Good news is I almost completely fixed it. Bad news is - any minute now my E string is going to crack.
Good news: Sanding worked big time. E string is now identical volume to A and G. The bottom of the saddle was indeed not "perfect". I could feel bumps. It was not a smooth surface. So now, the only thing left is that the D is a little louder than all the rest. Much less noticeable situation than what I had previously. Definitely improved the situation.
Bad news: we are able to use these strings even though they are not cut to this scale - because they are pretty soft. But, once I took the string completely off and put it back on, I now have damage on the E string, and I don't know if it is going to be stable. Kinda looks like it is going to stretch and crack. And - I don't have a spare set. One is on the way, but, that's a whole other story.
I think I am going to try the Goldtone Silverbacks. I was worried about the significantly different gauges yielding crappy intonation, but I'm going to give them a try.
[I had something to do with the Silverbacks a few years ago.]
[bass string experimentation is expensive - anyone want to GoFundMe?

jk]