There was almost no customization for the cocos2d framework. We did that put riq is catching up too quickly. I would strongly recommend to post any enhancements in the forum and get the functionality into cocos2d. Otherwise its really hard to update cocos2d. We were basically on the trunk version all the time.
EDIT: Oh, almost forgot: There is one bigger change to Cocos and thats the Particle System. We added different features to it (like stopping the particles at a given y-coordinate for the blood on the ground) and implemented a particlemanager so that all particles are drawn in one batch. This gives a very noticeable performance improvement. We would share the code, but it is very far from perfect. I do not really like how I implemented it and its very specific.
We did more customization for Chipmunk. This is because it is meant to be general but we wanted it to be specific for our case to squeeze out all performance.
@all If you can leave a ranking/review on itunes, we really appreciate it.