A. I'd rather you hadn't stayed there for a long time.
B. I'd rather you didn't stay there for a long time.
Feedback When we need to express the idea when you want someone to do something in the present or future we usually use the construction [would rather + subject + Past Simple]. Other answers do not relate to the meaning.
C. I wish you stay there for a long time.
D. I wish you stayed there for a long time.