Hello,
1) Adjust your coding in the following file to match mine which will fix the position of the logo and the overlay issue.
Template.CSS - Line 919
#s5_logo {
background: url("../images/s5_logo.png") no-repeat scroll left top rgba(0, 0, 0, 0);
cursor: pointer;
float: left;
height: 130px;
margin-top: -50px;
position: absolute;
width: 308px;
}
2) Looks like you figured out the background issue already for the solid color