Uneven pupil size is not something to be ignored. Is your doctor aware that you're experiencing anisocoria? In not, see him/her ASAP.

As someone who endured a serious whiplash/TBI, I'd be terrified to allow anyone to manipulate my neck so aggressively.

When you sustain whiplash, it can take a long time for the internal swelling to subside. The swelling can actually limit your mobility and stabilize your neck. As you heal, the swelling goes down. This can lead to instability, especially as you've probably experienced some muscle atrophy. For that reason, some patients report an uptake in their symptoms months after the injury.

As an experiment, put on a cervical collar, for a couple hours, and see if your headache, etc... abates. If so, you may have an instability. If you're lucky, strengthening your neck, with isometric exercises, might be enough to bring relief.