I came from the Philippines and the documents needed for leaving is basically the minimum requirement of the place you're going to. At the airport, I remember being asked to present the MOFA form and the written pledge. They also asked for the completed QR code that I didn't have at first so let me share the code with you. Just in case you still have to! You just have to fill out the thing and at the end, there will be a QR code displayed and just take a screenshot of it for the person at the check in counter to scan. You will also need to scan that same QR code at one of the stations when you reach Japan.
When it comes to the documents that you have to bring, you don't have to have multiple copies of everything but in case you're clumsy like me, I suggest you make a copy just in case you lose it along the process of moving and stuff. I also suggest that you make a folder for the apps that you have to be dealing with when you're at the airport. I don't have an active Japan number then so what happened was they sent an email to know for sure that they can reach me in the email address I provided. So for those who are asking, you don't have to have a Japanese number for all of these. Although you STILL have to provide two Japanese numbers at one of the stations. In my case, I provided my dad's prepaid phone number and my friend's.
Fifth station is where you have to wait the longest. You have to wait for your number to be called which by the way they will assign to you at one of the stations. I just forgot what station they did that. They will ask you to put the sticker that has your number at the back of your passport and ask that you do not take it off during your quarantine.