You have to read 'My dear Waifu' in certain order iirc.
MDW's four endings work by reading each track all the way through, and then the fourth ending you get by reading 7 1's, 7 2's, and then 6 3's. You're saying you can alternate 1-2-3 and still get it? That's weird.
It doesn't work like that. Each girl in waifu book has a number of "dates" tied to specific chapters.
For Ms. Stevens it's 1, 4, 6, 7, 10, 13, 15, 16, 18.
For Shea its 1, 2, 6, 9, 10, 12, 14, 15, 17.
For Leena it's 4, 6, 7, 8, 10, 12, 13, 16, 18.
Your choice in chapter 20 decides your girl for the ending.
If you got at least 8 "dates" with Shea or Leena, or 7 with Ms. Stevens,
and choose them on chapter 20, you get their corresponding endings. (and if you finish with same girl again, genie will comment on that)
If you got less than 4 "dates", you get "anticlimactic" ending, with variation based on your choice in chapter 20.
If you got between 4-7 dates (4-6 for Ms. Stevens) you get anticlimactic ending with slight variation. (i.e. Shea will be home but goes to the prom with other guy)
For example, you can choose to "hang at school building" only in chapters 1,4,6,10,15,16,18 and 20, and you still end up with Ms. Stevens. Vice-versa you can choose school at 2,3,5,8,9,11,12,14,17,19,20 and you will still get anticlimactic ending.
For "Harem" ending you need to complete the book with each girl first, then on next read get at least 1 date with each girl. Order doesn't matter, as long as you got one date with each girl you can avoid them on purpose and still get harem ending.
You can always check github to see how all this works:
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