Just adding to what others said, I believe several players reported that with the Mod installed it's not possible to achieve the Jaye&Mal throuple. I haven't achieved it either, although I have to admit that I haven't started a playthrough from scratch but from earlier saves and followed all the steps. So, in my case, maybe the modification of love points before those saves impacted the outcome. Still, I don't think I have read from anyone using the mod that he/she managed to end up in the Jaye/Mal throuple.
Once the epilogue comes out, I'll probably play it from the beginning (skipping as much as possible) using the steps that
Justaphase and others have indicated - without the mod.