Missing script references like that point to a bigger problem that's well known in Unity.
Unity keeps references inside metadata files, which are by default hidden in the library folder. If you copy the Assets folder at any point, the metadata will not be copied with it, and all references will be broken.
You physically have to enable visible metadata files through the Editor settings in order to be able to copy things properly.
If you do happen to start a project with these broken references, and you start from scratch, you may not even realize that there is a problem until you follow the standard upgrading instructions which involve deleting the NGUI folder. At that point proper metadata files will be added, and since your project relies on newly-generated ones, everything will be broken again. Moral of the story -- always follow the same process. Either you do it as NGUI suggests, or you re-do the same thing you did last time (copying the files over).