That last part..
CODE
table table tr.caption td.index {visibility:visible}
table table tr.caption td.index a {visibility:visible}
That makes the top navigation show up, and most layouts actually use that. So if you're using custom navigation (you are) just remove that part cause you don't need it. :)
Oh, I'm not positive but I think you can get rid of the white background by making everything transparent and then specifying a background for the entries with like:
CODE
.entrybox table td{
background-color: ######;
}
.entrybox table td.caption, .entrybox table td.index, .entrybox table td.comments{
background: transparent;
}
Dunno if that will work, but you could try it.

(You'd need the second bit of code because the first part will actually make EVERYTHING have a background image, and the last will make everything but the entries transparent.)