I want to have the player be able to have buttons to click for the choices instead of links, but I don't know much coding and I can't figure out how to do it. If anyone here can tell me how that would be great, thanks.

The difference between a link and a button is just what it looks like.

If you don't want to modify the ShowMenu function, you can probably do something using javascript.
Immediately after displaying the menu, you could do JS.eval("$('."+game.menuoutputsection" a').css({SOME STYLE INFORMATION HERE});") to change what the links look like.

Or a little more complex, you could do:
JS.eval("var menusection = '."+game.menuoutputsection+"'; $(menusection+' a').each(function () { $('<button>', {type: 'button'}).append($(this)).appendTo($(menusection).last()); }); $(menusection).contents().filter(':not(button)').remove(); $(menusection).append($('<br>'))")

Still could use a little tweaking to make it look right, but it works on my quick test.

Do you mean make a function that will change the style of the show menu?

If so what parameters should I use for the function?

OOH, I'm such an idiot! You mean run a java script after the show menu