I had trouble with binocular vision after my concussion (getting both eyes to work together) though unlike you I didn't perceive that I was having trouble with it until testing showed problems. It definitely aggravated my headaches.

You should have a medical eye exam (which tests acuity, field of vision, etc) and also a Visual Efficiency Evaluation, which checks for how well your eyes work together.

I did ten weeks of vision therapy which helped a lot.

You can find an optometrist that does this type of testing and therapy here: http://www.braininjuries.org/

Good luck!