Learned this today: The style you're referencing is the box-shadow
on .navbar-inner, line 2335 in your bootstrap.css.
Added the following to my over-ride css for .navbar-inner:
-webkit-box-shadow: none;
-moz-box-shadow: none;
box-shadow: none;BUT I still get a black line across the top in IE9... AND would still like answers to #1 and #2 above... Thank you, Tom
