OO-style programming can help overcome some of the complexities you are experiencing.

From what you have described, I see 2 primary objects:
* Rule
* Target

Each of these will have properties and methods.

You could create other object classes that handle collections of these base objects, but initially, I'd suggest you keep that in your main code.

Inside the "Target" class, you can have a method to run a single RULE, and another method to run an array or RULEs. (Or you could reverse that, an have a RULE run on a set of Targets).

Once the basic underlying mechanics are setup, you can work on arrays of these objects.

You will not regret the decision to invest in learing the OO way. And we monks are here to help.