I'm filling out Form N-600 to claim U.S citizenship through my deceased mother. The form is suited to living parents and I have two questions about how to answer questions.
Part 2 of form:
Do I check off A(I have a U.S mother or U.S father) or D(other, explaining I have a deceased U.S mother?
Part 5 of form:
Do I list my father as my mother's current spouse? Or previous spouse?

The form says nothing about your parents being alive -- whether they are alive do not matter for your citizenship.

You should check A (I have a U.S mother or U.S father). You should not fill out Part 4 (since you are not claiming citizenship through your father). And in Part 5, you should fill out information about your real mother (the one who was a U.S. citizen), who is deceased. According to the instructions, in the "Home address" field, you should write "Deceased" and provide the date of death.