What strikes me on this clean tone is the unusual almost hear piercing brightness of the attacks, while the rest of the note sounds very much more like a strat’s neck pickup sound.
I’ve read that for this, Zappa might have used a very special digital reverb (a very new, cutting edge, thing at the time). I’ve also read that he might have set a piezo transducer in the neck of his strat. But there are some many legends around this tune !
As a first approach, I was tempted to use two compressors in parallel with different settings in order to isolate the attacks and push their brightness using a high pass filter before mixing back together the two channels.
On the distorted tone, one of the most striking feature is that “Ü” like “formant” (a U pronounced as the French do, or the sound “y” in the Inernational Phonetic Alphabet, or “Close front rounded vowel”).
I am using the term “formant” (that comes from phonetics) to identify this part of the tone as I think it helps identifying what’s going on with the signal.
It could possibly be obtained using a talk box. It is very much reminiscent of someone crying and weeping which obviously adds to the emotional aspect of the piece.
In terms of acoustics, it seems to correspond to applying a couple of narrow band-pass filter centered around (235Hz and 2100Hz).
I have done tests in the past which were kind of going into the right direction without totally satisfying me.
I have also read an article somewhere relating the position along the string where it is plucked and the produced sound in terms of overtones to phonetics “formant”. I will try to retreive it and add it to this discussion.