The 2nd-ary disciplines that are already created will need to be changed to be primary custom abilities, and we'll need to edit the name so that the user will understand that these are for the dual disciple archetype only (or make it available only to the dual disciple archetype -- which I think it may already be). Then we'll be able to use the 2nd-ary custom abilities for the additional discipline mythic ability, and the 3rd-ary custom abilities for the extra discipline power lists.
Maybe a look at how the Ranger Favoured Enemy class feature is implemented would help with this primary/secondary control?