You say you sanded the bottom of the saddle flat "with some improvement" which, if you have done this with due care and the sound is still poor, would lead me to think of two other possibilities.
One: maybe the Transducer is faulty and not 'reading' and converting vibrations equally along it's length & fitting another UST should rectify this particular problem or,
Two: Maybe the bottom of the bridge slot is not flat or it's walls not perpendicular to the bottom (causing the saddle to tilt forwards under string tension and not make full & proper contact with the transducer's face), you say the previous owner has played with saddle/action height perhaps they have also messed with the slot? Another possibility is, having worked on supposedly 'top' brand named instruments that are mass produced, quality control and machining processes aren't always at their best

and little flaws can creep in on individual instruments. The problem could have been built in from birth, the bridge slot may have escaped the quality controllers eye! Not the norm thank god but it does occasionally happen.
Just another couple of
possible area's to consider.