Hello, this is my first Jam and I never worked on an HTML file before. I decided to translate only the 5000 recommended words, but I'm a little unsure on what to do with the translated document. Should I leave the entire document with everything untranslated after the 5000 word mark or cut it and submit only what I translated?

Do whatever you think is best!
Remember there isn't a jury to decide what you can or can't do. Just your vision for the project and how it will be welcomed by the visitors on the site.
Make it yours & make it cool :)