Navigation menus integration issue

So I have googled and searched for the last several days for a solution for my navigation menu problem and after reading through and testing out various ideas and theories I have finally decided that my next course of action would be to ask a community directly for help.

The problem: I have two horizontal menus (one on the left, menu, and one on the right, menu2, with a logo separating the two of them). They each have their own css style file (which I believe i can just put into one file…). Once I installed the custom theme I had created, though, I discovered that the navigation menu will only display vertically as bulleted text. WordPress appears to not recognize my css file, for some reason. I am currently testing it through MAMP so it’s not available for online viewing; however, if there is still confusion after reading the code, I can upload a screen shot and submit all of the css.

What is it that I am missing or doing wrong? I deeply appreciate any words of advice. I have included below the code from my functions.php file and my header.php file.

Functions link:

Header link: