You say: I want to see your hands on your desk at all times. No more, no less. If he is not severely MR, he should get what you mean right away. I know teachers who have had to say this to main stream kids.
As to the touching the papers thing, do you think the other kids always wash their hands after doing anything? Not very many germs can live on paper - it;s an inhospitable environment for them. So, while it's a gross thought, don't worry about it too much.
I have gotten papers from kids with blood on them. (ick. I hand them back and ask for a re-do as it does not meet our team's minimum standards)