The exact mechanism for whiplash injury remains unknown. As you said, scientists have shown that muscle damage might be part of the acute symptoms, but muscles heal and recover during those first few weeks. Nerve root pain doesn't really cause the kind of symptoms whiplash sufferers report.
A more recent study looked at the impact of whiplash injury on the joints of the lower cervical spine. Facet joints at C4-5 were stressed under normal conditions. Then they were examined under whiplash conditions. The amount of extension was the same in both cases. The speed and shear motion were much greater in the cases of whiplash.
It looks like the stress on the joints and joint capsule may be the source of the problem. This type of information will help doctors, therapists, and chiropractors rethink treatment for symptoms from chronic whiplash injuries. More studies are needed to find out what kind of treatment works best for this problem.