I was having difficulty getting the menu dropdowns to work when using the jQuery library. But here's the fix.
In the menu.js file you need to change the variable "$" into something else. As you know, jQuery uses this variable as a critical element and will override this variable in any other scripts present when the page loads.
Inside menu.js there are two variables using "$", but only one needs to be changed. On line 106 you'll see where "$" the variable is declared. Change this to something else, like "$B". On line 110 you'll see the variable "$A", this is fine and can be left alone (hence why I renamed "$" to "$B", to keep some sort of convention.)
The variable "$" is called four more times. Change all of these to your new variable ("$B") They are found on lines 132, 201, 206, and 220.
Hope this helps anyone else!