#1
When I first started playing guitar I was practicing guitar like crazy and learning my scales, basics, and theory but lately all I do is just song write without learning new songs. Now that I'm going to graduate I need to get back my theory and playing knowledge.

What should I study now? What are some good pieces to study and what should I be studying to get into a good university?
#2
to tell you the truth just practice all of those scales. if you want some practice try a full fretboard scale run. and good luck.
#3
You know your strengths and weaknesses. You decide what you need to focus on to improve your knowledge.

As for getting into a university, be proactive; Speak to the universities you are interested in about what is required. Then work those requirements into your practice routines.