What should I do about my feeling of having committed forbidden acts by placing my father with my mother in a single grave, not moving him after the mistaken burial, and exposing them to insult from my mother's sisters by opening the grave, collecting their bones, and placing them in a new shroud and a pit inside the grave?

What is forbidden is the collection of deceased individuals in one grave without necessity. As for burying each deceased person in a separate grave, there is no harm in the graves being adjacent. Some scholars have permitted burying a man and a woman in one grave, provided there is a barrier between them. There is no harm in burying parents next to each other in the family cemetery. It is forbidden to exhume graves for benefit unless the bodies have completely decomposed and turned into dust. If a bone or any trace of the deceased remains, then it is not permissible to exhume the grave.