Script that creates an active CSS on link
Please consider that using Javascript might not be the best solution. If you use something like PHP, passing a variable to the file generating the html setting which one is active is a cleaner solution.

Anyway..

First it seems that the following variable is unused and can be removed:

var link = window.location.pathname;


Then this line:

var currentPageName = window.location.href.match(/[^\/]+$/)[0];


will trigger an error if the url is root (http://www.example.com/)
and it's the same as in these ifs, which also can be combined to one:

if (window.location.href.indexOf("R") &gt; -1) {
    var currentPageName = window.location.href.match(/[^\/]+$/)[0];
}

if (window.location.href.indexOf("C") &gt; -1) {
    var currentPageName = window.location.href.match(/[^\/]+$/)[0];
}


which means that one of them is redundant and can be removed. 

You can also remove var in all but the first  var currentPageName

An easier way to add the active effect would be to use the attribute contains selector like this:

selector = '.main-navigation ul li a[href*="'+currentPageName+'"]"'
$(selector).css({
    'color': 'white',
    'font-weight': 'bold',
}).addClass('active');


This means that the complete code could look like this:

var match = window.location.href.match(/[^\/]+$/);
var currentPageName = '';

if (location.pathname == '/') {
    currentPageName = 'MD';
} else if (match != null) {
    currentPageName = match[0];
}

var hl = $('#ih').val();

if (hl == 'True') {
    currentPageName = 'WVD';
}

selector = '.main-navigation ul li a[href*="'+currentPageName+'"]"'
$(selector).css({
    'color': 'white',
    'font-weight': 'bold',
}).addClass('active');