Good looking typesetting from markdown is surprisingly hard. Played with it a while myself, and it's really not fun.

.... is what I was going to say until I went and hit the print button and 10% of the text was missing and everything was right aligned in the top right corner.

Yikes. You may find it worthwhile to clone the repo, iterate over it with pandoc to make A Big HTML File and then use your browsers print feature or pandocs converter. That's about as good as you'll get without a lot of pain ime.

If you hide the left sidebar, and then print, then it is aligned correctly. Each H1 is on a separate page, which is certainly a choice, but on cursory inspection, it would seem as if all the content is there.