It sounds like your doing really good, but don't rush yourself. Take your time and really learn it and absorb it. Are you doing the listening technique also?? Anyways, your question. I would just work with one at a time, changing between clean and medium before you have it might confuse you. Get one down, I'd say at least 36 notes (3 octaves) on clean before attempting the others. The reason is the ear will go through different levels, getting deeper and deeper into the sound of a note. The first level is timbre (sound of an instrument). This is easy for the ear to become accustommed too, but it's takes listening at this level for so long before you can start hearing at different levels. So by changing timbre you are only adding on to the time it takes to reach the next level. For that reason I say stay with one until you master it.

Right now you probably are starting to notice something different in each note. So when you hear this little sound (whatever it is), you know what note it is. Maybe it's a buzzing or maybe the string vibrates a certain way. This is a good sign, but even this will eventually break down once you get into your second octave. Then you will notice the high E may not have that same clue, but you will notice something similar in the high and low E. When you can tell a note played in 2 seperate and different octaves. That's when you are really hearing the "color" of a pitch. By the time you get three octaves, pitch color should be developed in your ear. When you start to pick up on that sound, the notes on medium guitar will become easier to distinguish as well. Then other instruments, because pitch color never changes. The timbre does but that distinguishable sound is the same.

I'd suggest if you aren't, take some time playing the notes your practicing on your own guitar, and listening. Although eartune gets you to name the pitches you are still listening to a recording that plays exactly the same everytime. You should know that NO two notes, even played on the same instrument sound exactly the same. That could also be the reason why medium guitar is so much harder. Your ear is becoming only accustomed to the sounds on eartune. And I bet if someone would quiz you and play any note you have studied, having your ear only learning eartunes wavs. You might find yourself bewildered at was note is played.