So after a week of eliminating grass hay from her diet, limiting her pellets and switching her to primarily timothy hay she is no longer having diarrhea or excess cecal pellets and seems happy.
We also got her a black dwarf netherland to play with and they seem to get along pretty well. She's a lot more playful now and no longer poops or pees on the bed or random places and Leto our dwarf automatically started using the litter boxes. He's a pretty independent bunny.