About the Church storyline:
If Shanice & PriestBot went to the Vatican, came back, and you unlocked Shanice’s sexbot-module repair feature, that means you already reached the Good Ending of the Church route. There is currently nothing left to progress in that path other than some few wholesome event such as "Hanging out with Shanice".
About Melissa:
Her storyline does not go very deep yet. The latest available content is the scene where you hang out with her at the Bowling alley. There is no additional Melissa progression at the moment.
About the Doctor / Sanity path:
If you refused the doctor’s treatment at the very beginning of the game, you will not be able to enter the Sanity route later. So at around Day 52, I believe that there is no further progress you can make with the doctor storyline.
About Money and progressing the story:
To continue into the later parts of the game, you generally need around 1,000,000 $ or more.
This is because:
- The Rich Area requires 1M to unlock.
- The Rich Grocery lifetime membership also costs around 1M.
So having 1–2 million is enough to progress without issues.