Unfortunately, for the technical reasons given, there is no easy way to transcribe MULTI PART scores from mp3 or wav formats into midi or notes. Transcribing by ear is the only RELIABLE method.
I saw a good analogy elsewhere, here it is (reproduced) :- "you can easily make a cake out of milk, eggs, and sugar, but it's rather tough to make milk, eggs and sugar out of a cake".
The suggestion by allchopin, concerning Amazing Slowdowner, is a good one.
If you want to waste your time playing around with audio to midi/notes programmes, then try intelliscore (probably the best of the bunch)
https://www.intelliscore.net/ er . . . There is one other reliable way for changing an MP3 file into a MIDI file.
Here it is: (reproduced)
(1) Put your MP3 file onto a diskette.
(2) Give the diskette to someone who is really big, really mean, and preferably somewhat drunk.
(3) Have your friend say "This [censored] is a [censored] MIDI file, and if any of you [censored]s disagree, I'll [censored] your [censored]."
I'll leave it up to you to find which method works best . . .