Reddit reviews Unity 5 Game Optimization: Master performance optimization for Unity3D applications with tips and techniques that cover every aspect of the Unity3D Engine

The most important way I avoid confusing code is a message system where scripts interact not by referencing each other directly but send messages "to whomever it may concern." This could be 100 other scripts or none at all. Scripts that are listening for those particular messages get them and any relevant information, but are effectively agnostic of each other so really effective decoupling.

Basically the observer pattern as I understand the term. Lots of discussion of that idea in this post.

I use something similar to the MessageKit tool that prime31 references in the top post, one that I adapted from this book.

I don't use this for everything, I'm not opposed to just including a direct reference where it makes most sense. Occam's razor all the things.

If you use this along with the single responsibility principle when defining your classes, you have super concise classes that are easy to understand at first glance and very reusable.

You need to buy the book Unity 5 Game Optimization . Goes over things you've asked and more.