Main Page Hoover Color Doesn't Work

[afo]

The part I've highlighted in red is the issue. It's incorrect for what you want to do.

.sideBoxContent {
background-color: #F5F5F5;
padding: 0.4em;
}
.sideBoxContent a { 
color: #000000;
}
a:hover, #navsideBoxContentTOC ul li {
color: #990099;
}

a:hover refers to ALL links which is why your other links aren't the color you expect on hover. To restrict it to your sideboxes, it has to be as below:

.sideBoxContent {
background-color: #F5F5F5;
padding: 0.4em;
}
.sideBoxContent a { 
color: #000000;
}
.sideBoxContent a:hover, #navsideBoxContentTOC ul li {
color: #990099;
}