Regarding the errors in timing at the beginning of the quest, you could always correct them at the start of the second load from save, and act like that's how it always was. Either start off waking up at the new apartment on March 25th, or we play through the end of the hospital stay and the move to Mitakihara from March 16th.
https://docs.google.com/document/d/1IeZVgx8fYWUNM8AzWBhzYzAf1ZbHfuczMGYymdhLnEo/edit?usp=sharing