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You can disable it through Vantage > Includes > admin-bar.php - Just change the first line to return_false.

Upgrading the same theme should go smooth. If it doesn't include your menu after upgrade, go to appearance>menu and make sure that your menu is allocated on the left and hit save. Before you upgrade...

This is a Vantage theme limitation. I'm afraid it is not possible as long as we don't have dynamic content size control yet. But you might not want to display each and every category on the sidebar...

You can create a new menu called for instance "Categories", add all the categories you want from the left to the menu, save it. Go to widgets, choose "custom menu", drag into any sidebar area, select...