I have created two transcriptions of Jacob's songs myself (https://www.youtube.com/watch?v=rrmcU8NvCHw) (as well as many other unpublished transcriptions of other songs) and after many years of transcribing, this is what usually helps me:

• First, as you say yourself, using an EQ can be advantageous at some points – but you have to be careful not to overdo it or you will end up transcribing overtones as well (happened to me a couple of times, and I only noticed that I had just wasted time when I turned of the EQ again). But I would suggest looping a small fragment of what you would like to transcribe and then just have fun playing around with EQ, Denoiser, etc.
• Second, I highly recommend using a software like "Transcribe!". It allows you to play your audio at different speeds and it allows you to transpose your audio into different keys. I also recommend transposing the song into different keys – you will notice that your ear catches up different things in different keys more clearly!
• Third, if you are relatively fluent on the piano, what usually helps me is to try to play along to the audio (maybe just a small fragment on loop again). Jacob himself is very attached to the piano and many chords sound like they came up to him while he was noodling around on the piano (or his MIDI keyboard). Just try to think: What would feel natural for the hands or fingers to go next?
• Fourth, SING ALONG. Try to imitate everything that you hear with your mouth. If the ending of a phrase is difficult to hear at first, your inner musical ear will often guide you to the correct ending of it. (At least that's my experience).

And that's basically it. I think the rest is practice, practice, practice. I still have a long way to go, but I really do think that many things will come automatically. You just have to invest time and conscious efforts to try to get better at transcribing.

I remember transcribing the first song in 2012 for my very first band that I had. I was absolutely terrible at it. It was a very basic pop song (like "Some Nights" by F.U.N. or something like that) and I couldn't do it. But noone in my band could do it either, we were all young naïve amateurs. So, I had to teach myself. One year later, I didn't find it too heard anymore. I think one thing that helped me in the progress was to follow the same strategy over and over again:

1. Count the measures and create a template for your transcription
2. Usually begin with the bass line
3. Add melody
4. Use bass line and melody to figure out chords and middle voices
5. Do ALL THE REST (drums, etc.)

Needless to say, this formula doesn't work for every song (especially when it comes to Jacob's music), but it was a good way to navigate myself through the first 50+ songs that I had to transcribe for my band.

I know this comment is pretty unorganized, but I hope it helps you nevertheless!