I also want to save the font size in my .emacs file.
Here's a snippet that lets you directly specify the global font size using an interactive function:
(defun set-font-size ()
"Set the font size."
(interactive)
(set-face-attribute
'default nil :height
(string-to-number
(read-string "Font size: " (number-to-string (face-attribute 'default :height nil))))))