Assuming the hadiths are authentic (we don’t claim all hadiths in al-Kafi are authentic) then here’s how we understand them:
1- As for the first hadith, it means the Qur’an with its original sequence and Tafsir. Only Imam Ali (a) wrote that and gathered that. Not only would he write down the verse, but he had written the Prophet’s explanation of it too.
2- As for the second hadith, it doesn’t state the Qur’an is missing or changed. He just says that the Mahdi (a) will bring forth the copy of Imam Ali (a).
3- As for the third one, it refers to the Tafsir. That’s how it was revealed meaning Jibra’eel explain that it was about Imam Ali (a). So it’s like between parentheses as an explanatory statement.