It looks like you've pretty heavily edited the code already, so I'm not sure how to get exactly what you want, but I have isolated all of the variables you want to change.

Centered Infobox and Quicklinks
Go into the Forum Wrapper and get rid of the table surrounding the infobox & quicklinks. All you need is everything in the <div class="sp-slideshow">. Then, go into the CSS and find the styling for .sp-slideshow and change the margin to be auto like this: 

.sp-slideshow{position:relative;width:500px;height:275px;margin:30px auto;}
The 30px part sets the top and bottom margins.

Moving the Navigation Bar
So, it looks like it's using an old version of sticky navigation. You need to change the top value in both #theFixed in the CSS and this script at the top of the Board Wrapper.

#theFixed{position:fixed;top:320px;width:100%;z-index:1002}

       <script>$(window).scroll(function(){
   $("#theFixed").css("top",Math.max(0,320-$(this).scrollTop()));
});
       </script>

With the above changes to the code I was able to get the base code looking like this:



Hope that helps!