One thing you should probably do to your site (if your prof cares about validating html) is change your script so that any element that appears multiple times uses a class, not an id. For example, you've got a ton of elements with id="modbox". Having multiple items with the same id doesn't usually muck up browser rendering, but it can really fuck up javascript. Just change the 'id' to 'class', and, in the css, change the appropriate '#' to a '.'. A great way to check for things like this is to run it through the W3 validator.

I changed the buttons a bit:

Right now your buttons look like this:
<a id="menufloat" href="?page=search"><img src="../resources/searchbutton.png"/></a>

The new styles work like this:
<a class="button" href="?page=search">Search For Mods</a>

You'll also need to change your id="menufloat" to class="button" which is a little more semantic. Obviously you can now make buttons with any text you want without messing around in a graphics program.

I haven't validated the css, and didn't change anything that I didn't know what it did. The CSS3 is kinda semi-prefixed, but if you know what browser your prof is using, and you feel like being really thorough, you can test it in that and add prefixes/shims as necessary.

I also changes your "Put your mod info text here" textarea, getting rid of the ????, and putting them in the css instead. It's good practice to separate content and presentation anyways :)