Yanking a couple of articles that make up a tiny amount of your traffic should not be a problem unless those articles have a lot of links or other off-site assets or unless those 0.51% of visitors do a lot of buying.

If you are worried about this, have someone write same-topic replacement content and toss it up on the same URL

I bought a domain that had about 25% infringed articles.  I took them down right away and tossed up replacement content and the rankings held.

The little box you talking about.

Make a small table or div and float it to left.

When you say duplicate menu at the bottom, do you mean main menu or sidebar menu.

You can do either.  Anything you want.

The hard bit is that nobody on mobile devices are using sidebar and that means people visit one page and leave without exploring any additional resources.

Go to a few of your pages and find opportunities to link to your own content.

• As the hypertext that wikipedia overuses in some people's opinion.
• In little boxes that float to the left side of your mobile pages (use images and text that elicit clicks)
• As a large menu of related articles at the bottom of your page (look at the provocative images presented in the Outbrain, Taboola, and similar widgets - you don't have to be nasty or naughty like some of them - there are many other ways to earn a click)
• in a search box at the bottom of your article and invite readers to use it
• you don't need a sidebar to entice people to visit another page... just show them what you have that is relevant, what is popular, what is new, what is outrageous - depending upon your audience.
• duplicate your menu at bottom of the page