Developing perfect pitch on guitar vs. other instruments: the timbre problem
I think guitar and other string instruments may present a special kind of difficulty that Burge doesn't really address in the course. This is the fact that the guitar actually has various small differences in timbre. Burge talks about how timbre can affect perception of the colors and can make it difficult to detect them on other instruments, but he doesn't mention that various timbres exist within the guitar. For example, take the note F# on the D string, 4th fret. You might be able to hear the special quality, the color, that that note has at that location. Take that same note on the A string 9th fret. Notice anything? The note on the 9th fret will sound a bit different - this is a tonality difference, or a timbre difference, and it will present a difficulty in gaining perfect pitch on the guitar. As we know, there are many such cases where the same notes can be played on three different places on the guitar. Piano players don't have this problem, although I'm sure there are other subtleties in developing AP on a piano.

How to get around it:
One thing I've noticed that helps is to take two strings, and play the note you are training on each one, back and forth. If you hear the color better on one string, play that one a number of times and then try to "transfer" your hearing of it to the note on the other string. You can do this for a few notes at a time too. I think you will notice that the B and high E strings don't have too much of a timbre difference, so those won't be very difficult to distinguish.
Burge has guitarists train open strings then random notes quite a bit. This is all well and good, but it will take you away from the timbre problem if you are continually playing random notes in random places. Instead, try identifying notes on first the high E string a bit, then the B string, then G, etc. You can go in reverse order, from the low E string, start from the middle, and eventually work up to random strings. Acknowledging the timbre problem and addressing it in this way is going to help you.

Important concept:
If it is helping your ear, keep training it. This may sound obvious, but in the past I have had problems with it. Something may have been helping my ear along, but because I thought I needed to train something else, I moved on too quickly. Try not to let this happen. If you are benefitting from training only two or three notes for even 5 whole minutes, that's fine. Also try going up and down a scale until you find a note that sort of hits a sweet spot with your ear. Train that note and the adjacent scalar tones. I try to avoid training three half steps in a row most of the time because I find it confuses my ear. Try doing a half step then a whole step. Train those three tones, compare them to each other, and move on to another section of the guitar, when you are ready. Also, going down or up an octave from the note you are training can sometimes help.

What do I mean by helping your ear:
Remember what I said about that little popping sensation you might get in your ear? This is good, just remember to stay relaxed as you train your ear, as Burge says again and again in his course. The sort of popping/opening sensation is your ear expanding and opening up, and it can only do that if it is relaxed (other people have described their experience differently than I have, referring to a feeling like they were putting on glasses (for their ears) when they didn't even know they needed them). How do you relax your ear exactly? I'm not really sure but I suppose one way to describe it is by saying just don't strain to try very hard to hear pitch colors. Try instead to let the sound come to your ear. That's the best I can describe it and honestly I often question whether I am relaxing or not while I'm training. I must be doing  it sometimes though because my ear is still getting better.
If an opening sensation becomes particularly active while you are training something on the guitar, keep training that! Do it until you feel you aren't really getting much out of it anymore, (up to about 3-5 minutes I'd say is reasonable). Conversely, if you start training some notes and you don't feel like you're getting anything out of it, stick with it for a bit and see if you start to get a slight opening up sensation.
These will often be subtle sensations, and sometimes you actually might not even have any. This is ok, and as Burge says, progress might not ostensibly come every day, but it is happening. He makes a nice analogy of the idea of a plateau; sometimes you feel like you've reached one, but it is at that point that you just have to walk across the flat surface until you get to the next hill that you can climb.
Sometimes I feel like I have hill days, and sometimes flat surface days. Actually for a while it's been basically every other day a little hill day and the other ones flat surface days. I hope the analogy makes sense.
One positive thing is that your ear seems to improve in between training sessions. It will seem to be undergoing changes - this is sort of your ear reassembling itself to adapt to a changing environment. You might only train 30 minutes a day, but your ear will continue to develop for the remaining 23 and 1/2 hours!