1. If you are in D Dorian, you need to start the progression with a D chord - either D and D, or D and A. As the cantus firmus is in the upper voice, you can't use the note A in the counterpoint, as this would give a perfect 4th (dissonant). Using G and D (as a perfect 5th) is not allowed as it essentially establishes a G mode. Therefore, the only possible note is D.
2. In the example, mi is F and fa is B. They represent a tritone, i.e. there are three tones (six semitones) between them. In the major scale, i.e. C Ionian, it's the 4th note against the 7th note. In D Dorian, it's the 3rd note against the 6th note, etc.
I was disappointed that the book didn't go into more detail about this. In the example, it's an upward skip from F to B that is marked as incorrect, however, what about going down from B to F? And what about going up from B to F (it's still a tritone, but in a different context), or down from F to B? I chose to avoid them all, although some clarity would have been nice.
3. The upper voices are only reckoned with the bass, but not with each other, so you're essentially looking, with 1-3-6, at a 3rd and a 6th; 1-5-8 is a 5th and an octave, etc. However, in my understanding the rules for voice leading are still to be observed between all voices, no fifths or octaves by direct motion, no "battuta", etc.
Chris