Mulligans is a general reference so be a bit more specific which techniques you have chosen to use. I have found MWM's from Mulligan are very useful in treating whiplash. It is common that this approach will restore range but can lead to some discomfort. Therefore you should consider finishing a treatment session with something pain relieving, e.g. some interferrential or perhaps even some ultrasound paraspinally.
Assuming there is no boney lesion (checked via xray,scan etc) your are really dealing with significant ligamentous damage (+/- discal damage), much like a badly sprained ankle. Heat on a sprained ankle might increase that deep noring pain?
The heat isn't really that useful here as the pain is probably deeper ligamentous pain. Isometrics in various ranges of rotation would be better than static isometrics in neutral. Also McKenzies supine exercise with a towel where the client lifts the head slightly off the floor in midline (using the towel as a cradle for the head), then does a retraction into the towel (isometric contraction) and then while maintaining the retraction pressure uses the towel via the arms to rotate the head through range is a great home exercise.
Sounds like you are on the right track but maybe are simply being a little to vigorous with your technique application.