Absolutely knots can cause that pain. I've experienced a similar situation.
the CT would of seen that. Plus, while it can happen, lung cancer will have more than just localized pain, usually people have pain, shortness of breath a cough etc. but not always. Your Dr.s have no reason to lie to you, they cant its law. That said do you sleep weird, lean on one arm or elbow when typing or driving. Do you play sports like tennis? These could all be the cause of it. I have terrible pain in my shoulder that was from a Tron ligament in the rear shoulder. ulnar collateral ligament, as it were. didn't even know it was torn, and didn't hurt to move it, just starting hurting when I woke up because I was sleeping weird. If you don't like what your Dr is saying ask for a second opinion, or go to another Dr. Most insurance plans let you go to a specialist without a consult, if that is you then try one. And yes, your traps can cause Terrible Pain, NFL players have missed games because of it.
good luck
You would probably benefit from gentle specific exercises as instructed by a physiotherapist and a massage.
Massage is really good to help relieve the tension that is caused by the knotted muscles. Arnica message oil or your preferred aromatherapy oil mixed with a carrier oil will help. You can also have warm baths with a body muscle relaxant to help ease the tension.
Knotted muscles can cause lots of problems, causing spasms and pain and also referred pain to a different part of the body.
As your xrays and CT scans came back clear there is no point wasting time and money for further tests. If you develop other symptoms regarding your breathing, a severe cough with blood, then go back and see the doctor.