First, a hearty
thank you for doing this!
Second, I believe that Dianae has the right of it.
- Level 01: Take the highest save of the two classes in each category.
- Level 02: Take the highest save of the two new classes in each category (so +1 CON/+1WIS from Monk and +2 REF from Ninja).
Confusion about things like this is one of the reason I allow only one Gestalt class in my games where I use these rules. So in my games, using the current example, a character could take their first level as a Gestalt Monk//Fighter. If they wished to multiclass, any multiclass levels would only be from one class (So they could be a Gestalt 01/Wizard 02, or a Gestalt 03/Wizard 01, for example). Will your system support this as well?