The dr to me I had pharyngitis and I've been taking the antibiotic but not been taking the Motrin she prescribed and now I'm having pain (almost like just being sore) in my shoulders and neck and a little bit in my jaw is this normal? I have had mono 2 and strep throat I can even count so I'm kind of wondering if this is really pharyngitis or if it's mono again.

Why do you doubt your doctor's diagnosis. More pertinent is why you're asking a random group of anonymous internet dwellers, who have precious little medical training, as a second guess of your doctor. The motrin was probably to help with the pain you're experiencing. You're not taking it, so you're experiencing pain.

I don't see why it wouldn't be pharyngitis.

I've had similar jaw, neck, shoulder stiffness and soreness from flu, mono, and Lyme disease. It's common. The Lyme was the worst as far as my jaw not working.

Any medical condition ending in '-itis' is somewhat catch all, because '-itis' just means inflammation. Sure, you could have more than an inflamed pharynx. Mono includes swollen lymph nodes around the back of the head, under the jaw, and so on, so did the doctor feel all around? Did you tell her you've had mono?
Take the Motrin and continue with the antibiotics, and let the doctor's office know if anything is unusual or might have been missed.
YOU need to be the informed patient. Read all about the conditions a doctor tells you you have, but keep trust in your doctor unless you have reason not to.