For the menu if you want to remove just the lines you can open template.css and go to line 754 and remove whats highlighted in red.
#ja-mainnavwrap {
background:transparent url(../images/trans-bg1.png) repeat scroll 0 0;
border-bottom:1px solid #6B3C27;
border-top:1px solid #6B3C27;
}
If you want to remove the whole transparent menu section that goes across the page remove background also.
For the footer same thing. template.css line 1010
#ja-footerwrap {
background:transparent url(../images/footer-bg.jpg) no-repeat scroll center top;
border-top:1px solid #46221A;
clear:both;
padding:15px 0 30px;
}