From your rules above...
Some are Innocents; the remaining are 2 groups of Mafia (Old School/New School); the Mafia will be divided into 2 teams and only know who is in their respective group; they can communicate only with their own group. Each group will get 3 investigations, if they find a member of the other Mafia group they will show as an Innocent.
and....
Each Mafia group will get an investigation per night, it will show mafia, but the Don will show as innocent the first 2 game days.
I think with yourrule change, you just forgot to change the first part.
Some are Innocents; the remaining are 2 groups of Mafia (Old School/New School); the Mafia will be divided into 2 teams and only know who is in their respective group; they can communicate only with their own group. Each group will get 3 investigations, if they find a member of the other Mafia group they will show as an Innocent.
and....
Each Mafia group will get an investigation per night, it will show mafia, but the Don will show as innocent the first 2 game days.
I think with yourrule change, you just forgot to change the first part.