I would start by first focusing on audiating specific intervals. Pick one to start with - say a perfect fifth. Since you are comfortable with intervals and can audiate individual notes, start by audiating a tone and then audiating, separately, a perfect fifth above it, just as if you were auditing 2 notes in a melody. Then, try audiating the first note, and hold it in your mind while you simultaneously audiate the second one. If you get stuck, audiate them in sequence a couple of times before going back to trying to audiate them together.
If you have access to a keyboard, you might also try playing the interval, and then audiating it, and vice versa - try audiating it and then playing it to check to see if it matches what you heard in your head.
Once you've gotten comfortable doing this with one interval, practice another until you are comfortable with all of the intervals. From there, you could move on to triads and then more complex chords. Once you gotten comfortable with this, you could try working with an organ score. If you get stuck on a particular chord, just figure out what intervals make up the chord, audiate the notes individually and then put them together.
Also, can you hear songs that you really like and know well in your head? If so, then you are able to audiate chords; you're just not practiced at doing so consciously. I do believe that if you can audiate one note, you can do two or more...like everything else, it takes practice. Practicing a little bit every day will probably lead to the best results.
