I agree with you that MKII is the best MK in the series (at least until MK9). And the MSDOS version of MKII is indeed the best (outside of Arcade). However, I have to correct you - the CD version had no Redbook Audio (not the first time I hear this erroneous claim). It was actually pretty much identical to the floppy version (unlike the CD vs floppy releases of the first MK).
In general, music-wise, the first two MK games are very interesting:
MK1 floppy version - dual soundtracks: Adlib or Roland MT-32/LAPC-I (the latter is heavily slowed down for reasons unknown) MK1 CD version - digitally recorded music - identical to the Arcade, except at lower sampling rate
MK2 (floppy/CD) has 5(!) different soundtracks: Adlib/Sound Blaster, Sound Blaster AWE32, Gravis Ultrasound, Roland MT-32/LAPC-I and Roland SCC-1 (General Midi). Each is a bit unique.