If there had been a prior traumatic injury to her head that resulted in this extensive surgery: i.e.: removal of her eyes, missing teeth and lips than there is a possibility that her brain received trauma. Brain trauma can result in epileptic seizures. Seizures can occur anytime and may even occur when the patient is sleeping. Running in her sleep does sounds like very vivid dreaming, or night terrors. Obviously the poor girl has been through a lot so it is possible that she could have night terrors.
However, there still could be something wrong neurologically with your cat's brain, and unfortunately, the only way to determine this definitively would be with a brain scan, such as a CT or MRI or equivalent, and possibly analysis of cerebral spinal fluid and other sophisticated diagnostics. These would require general anesthesia. If the results are all normal it could still be idiopathic epilepsy.
It would be best to try to make sure that she is in a safe place when she sleeps so that she does not injury herself. That may be difficult if your bed is situated high off the floor. You could provide a comfortable kitty bed on the floor for her.
Thank you so much for your responce. Thankfully she only does the twitches and running in her sleep so it does seem like night terrors. If I notice it getting worse then I'll see about getting the scans done. I'll let her doc know at her last visit. Thanks again for the help.