So I wanted to start a Masters program but they require that I have Calculus III. I want to take that course at the university, but I need to be ready for it. As I look at Khan Academy and do some of the exercises for pre-calc, I realize I am so far out of school that I need to study areas of math even prior to pre-calc. Is there an assessment of some sort online that would help guide me to what I need to focus on or should I just work through Khan Academy material? Any thoughts?
I can share my experience as to your pre-caclulus question as I have just recently finished precalculus about a month ago and about to finish Calculus I now (not the rigorous type, and also I am assuming you are not looking for that kind of a review).
I would suggest checking out a standard text like Stewart's Calculus (whether through a library or some other means) as it has a diagnostic test in the beginning that covers an array of precalculus topics like geometry, trigonometry, functions, and others - whatever you don't understand here or are not confident with will basically tell you what precalculus topics you need to review (the Early Transcendental edition of Stewart even delves into precalculus topics for the first chapter). I would prefer using Stewart over Khan Academy as it has more questions and even slightly challenging ones towards the end of the exercises. I think Khan Academy may help in aiding understanding some concepts you may have difficulty with but does not provide enough practice in applying the concepts you just learned (at least in applying them in various ways).
In case you are looking for an exam, try the 1998 version of calculus AB exam,(http://apcentral.collegeboard.com/apc/public/repository/calculcus-free-exam-1998.pdf)
It should provide you with some insight on which area you need to work on.
You mentioned you want to take a master program, I am assuming the course is advanced Undergraduate course, and I believe "Calculus" by Michael Spivak would be the perfect introduction book.It assume literally no prior knowledge of calculus and is used by our university as a text book for pure math major.
Schaum's Outline Theory and Problems of First Year College Math (1958, Frank Ayres)
As with most Sahum's, it is down to earth (simple words). Not terse or "math mature" but also not loquacious. Has the answers to the problems (designed for self study, not for selling to paid instructors). Covers Algebra 1 (linear equations), Algebra 2 (quadratics, logs and exponents, etc.), trig. analytical geometry. And has a short, friendly intro to calculus.
Furthermore it is written for people in your situation. You have had the courses before but don't remember them, maybe even didn't do well the first time through and/or are not a genius. But it will help you to time efficiently refresh your knowledge or bridge gaps you always had.