Adding a Javascript menu to a popup/modal?

I am having the weirdest problem. I am setting up my portfolio and I need to show a number of Javascript menu’s I have created. However these menu’s require me to add a string in between the head tags.

Well I have tried and I can’t get it done in WP.

Now I came up with the idea of having a link in the portfolio to a pop-up that shows the menu. However this results in the same problem. When I want to show the menu in a simple html page I will need to set the height and width of the pop-up window and remove some of the toolbars. To do that I again need to place code in between the head tags in WP because this is accomplished through Javascript.

So now I am lost and have no idea how to solve this.

Would anyone know a creative solution?