A.S.
Your post struck a chord with me because I frequently get the Sunday "funk" - and I think it goes back to my childhood. The weird thing is I loved school until high school.
I was (and still am) emotional and somewhat anxious too. I still managed to make it through college (which I loved - I just hated high school) and grad school just fine.
I would try to make Monday afternoons super nurturing. Perhaps make brownies after school, or something she really likes. Celebrate her getting off to a good start for the week. Don't let younger sister minimize her feelings. Just really praise her for all the growth and progress that she's making.
I might also consider homeschooling. My older son hated school from day one, even though he is a good student, good athlete, and well-liked by his peers. He joined my younger son and I (who started homeschooling a few years prior) in 10th grade and just really blossomed. School is not a great fit for all kids. I hate to see their genuine and innate love of learning quashed.
Good luck and I hope you can get this under control.