If you change line 17 of templates/common/navbar.tpl from:
<li id="userHome"><a href="{url journal="index" page="user"}">{translate key="navigation.userHome"}</a></li>
to
<li id="userHome"><a href="{url page="user"}">{translate key="navigation.userHome"}</a></li>
when you click on the “User Home” link in the main navigation bar, instead of directing you to the Site’s User Home, it will direct you to the Journal’s User Home.
I expect this to resolve the first problem you describe here: