No as long as your article is at least more than 30% percent unique you will be ok. Or more unique original content than copied content you will not be penalized and it will get indexed.

1. As far I know about duplicates I don't think so javascripts come in the category that could be penalized if used more than one page.

2. If you mean having a table of 1 row and 3 columns that also used in other pages as well then the content used in that table comes in play. I am sure you are not talking to have a blank table it should has some content. If it has any kind of statistical data and used in other pages as well then I think won't penalized because one could have a data set that needs to be presented on several pages. But if in that table a pure wordy content then in my humble opinion it might penalized.

3. You can have identical side menu on multiple pages infect it's a common practice to have identical side menu on most of the pages of a site.

Search engines are quite clever at detecting screen 'furniture' nowadays, so you don't need to worry.

Your menus should be in the same position throughout your website - that's good practise.

Certain elements on your page should be the same on every page of your site as it is disorienting for the visitor if stuff moves around, disappears or has no logic.

The main body text content of your pages is what matters. That should not be the same on all pages.