What Monarch Watch research suggested to me is to lay the pupa on its side or back so the head, legs & proboscis are upwards on paper towelling. I use newspaper, making a crease for the chrysalis to lie in. Then take a small strip of fiberglass screening, 3" x 4" and roll it inside a large clear plastic cup & cover the chrysalis. When the butterfly ecloses, it will climb up the screening but being separate from others, it won't infect others should it be diseased. A roll of 24" wide fiberglass cost $5, clear plastic cups are everywhere. They don't need that much oxygen so you don't have to puncture the cup and the screening & cup can be sterilized & reused.
If you don't want to separate the pupa from the top of your container, at least give it something to crawl up on so it has a chance for those beautiful wings to unfurl and dry. A rough stick or a piece of screen up the side will give it a ladder. Seems that 2 friends have had ruined monarchs because they fell in slick plastic container & couldn't climb up the walls to properly set for those wings to develop.