1. All the items in the combobox have the same template, that's why I would suggest to try to bind Visibility property of the checkbox and use some ValueConverter.
2. You could update the IsSelected property of the item in SelectionChanged event handler.
I've attached an example demonstrating how you can implement both requirements, please download it and give it a try.
3. HtmlPlaceholder control is rendered over the Silverlight plugin, so it is not possible to show the combobox over it.
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