We'd like to display individual knowledgebase articles embedded within an application we have created. Is there a way to get the article content without the portal header, sidebar etc.?
You can use the DeskPRO API to retrieve article content. Your app or site can make a REST API call and get the content of an article in HTML, which you can then display. See the Developer Manual for how to use the API in general and details of how to retrieve articles.