Based on what I've seen elsewhere, I got a hunch that perhaps these routes had to be played consecutively on the same save file, and that worked! I'm so excited to read it!
Hi thiswasnttaken!
Thanks for playing the game and I'm glad you're enjoying it.
Yes, you will need to get two friendship endings one after the other (can be both boys or Emily and one of the boys, doesn't matter). Once you finish one of the friendship endings it will prompt you to try again after the credits, continue from there.
Best of luck!