Roughly 4-5 months ago while in Afghanistan I was involved in an incident that caused a severe 'whiplash' effect, and my neck never went back to normal. Everyday after that I would wake up with a sore neck that would snap and pop a lot, and then a stiff/painful neck throughout the day, with the pain varying from day to do. The most painful movement is to look directly up. I never sought medical treatment, as it wasn't exactly a possibility given my situation.

I returned about a month ago, and a little over a week ago I was involved in a car accident (rear ended, the car I was in was totaled). I was taking to the ER, given a CT scan, and all that was found was a shifted vertebrae. I was sent home with basic painkillers (ibuprofen, aspirin), and none of it helped. I went to sick call a few days later (being in the military you can't just go to a real doctor), they gave me a few muscle relaxers and sent me back.

Now, the pain has not subsided at all, and I am out of the worthless painkillers I was given. When I sit in a chair for too long there is a burning sensation at the base of my neck, right between the shoulders id say. Other than that, just general pain, and like I mentioned before the most painful action is looking up. And it does effect my sleep because it is very uncomfortable.

Basically, I have a couple questions. Is this most likely muscular? In what cases would a shifted vertebrae be normal (thats what the doc told me)? Should I seek further medical attention?

I would have already scheduled an appt but I'm getting the runaround and it is extremely difficult to get an appt with a real doc.

Get the CT scan and take it to a chiropractor. He or she will see you for an initial exam to see if you would be helped there. Certain conditions won't be, but others will get better treatment than with an MD.
Injuries can do many things to the spine that don't show easily. One is a bruise (that never rises to the surface), a clump of blood that dries and presses on a nerve. A nerve can pinch from slight movement of a vertebrae, and fluid can leak out of the sac that protects each vertebrae from rasping against the next one.
They are supposed to give you any scan if you request it, but I don't know about the military - they might not, having their own rules. But go to a chiropractor.
Moist heat is the best treatment other than painkillers, for now.

An MD will treat you with pain killers and muscle relaxants and maybe send you for PT -- diathermy (heat) and intermittent traction (on and off in a repeated cycle). As Joy says, a more immediate solution would be to go to a good chiropractor who can adjust your neck and do all that a physical therapist can but much more quickly.

When I had a CTL x-ray set, my doctor could tell that I was in several car accidents. I had slight whiplash in one or two of those. So what can I say? It is possible that you've picked up a neck injury, mostly soft tissue, from that incident. No bone damage, but things aren't aligned.

Your back and neck are a column of bones and discs. They fit together like a stack of pennies and are just as stable as one too. The key to keeping it all together is the liagments, muscles, and tendons that surround the structure like sheath. This allows you to bend and move like you do. When you have trauma to this structure you can experience a whole lot of funky things.

As previously suggested a chiropractor or physiotherapist would be the best way to go. I am not sure if you can get a refferal to them in the army but try as hard as possible. Pain killers and muscle relaxants are short term and not permanent. Trust me I know this through experience.