Actually the Custom series tames the highs a bit. I would maybe try the Custom Custom which is pretty dark, or the newer Custom 5. They might do the trick. As for the sound difference, I haven't seen one of the FG flame tops but I would imagine it's a veneer like all the other "S" series with flame tops. The body is so thin already that you'd be practically dividing it in half to do a real maple top. So the sound is more mahogany, but mahogany is not bright. The thin "S" body is thinner and more squeaky sounding to me, though. I have a few "S" guitars and I think if it was made out of anything other than mahogany it would sound like a tin can. There are tolerances between same model pickups, but you are likely experiencing the guitar differences.
If you don't mind the look of the original Trembucker it's really an underrated, "sleeper" of a pickup. I would be great in an "S" body.