If possible include all your javascript at the bottom of the page. The longer you delay the download and execution of your scripts the faster your page will appear to the user. Perception is reality and if you can gain a 10-20 millisecond increase just by putting your javascript at the bottom of the page it is huge in the users eyes.
One thing you don’t want to hide on your homepage is the search box. Users who cannot find something in the first 15 seconds on your homepage will often use the internal search. If they cannot find it they will probably use their first instinct to use Google. If you pages don’t rank well on Google or their favorite search engine you could be at a loss.
Since the economy is a major factor in the decision to continue education it is a great idea to put the tuition and fee information right on the same page as the program information. This way a prospective student does not have to go fishing around your site looking for it after they decided you have the program they want. In addition having direct links or copy about financial aid or scholarships to ease the process.
There is no point in having a sub menu with only one item in it. If this is the case make the main menu link go directly to that page. This reduces a click and a possible point of frustration/confusion for the user. It may take the developers of the site an hour or two to make this action happen but that is nothing compared to the thousands of people who visit your site as they navigate through it.