Probably because my blog is a subdomain these issues never came up before.
Change the site.master page
1) Replace
<link rel="shortcut icon" href="~/themes/Thumper/images/theme_icon.ico" type="image/x-icon"/>
With
<link rel="shortcut icon" href="images/theme_icon.ico"
type="image/x-icon"/>
after creating an images folder off the root and copying the theme_icon.ico there. But makes it not so generic.
2) Change
<span class="sitename"><a id="A1" href="~/"><%=BlogSettings.Instance.Name %></a></span>
to
<span class="sitename"><a id="A1" href="<%=VirtualPathUtility.ToAbsolute("~/")%>"><%=BlogSettings.Instance.Name
%></a></span>
3) In stablestart.css
margin : 55px
auto;
Becomes
margin : 0
55px auto;
because we don't like to waste space at the top.