HI there... Christine here has had a mandiblectomy and may be a close fit for your situation. However, I think maybe I can help a bit.

First of all it says you have wasting of the scapula/shoulder etc. This is definitely from the neck dissection as they cut the neck muscles during the surgery. I know you have been to therapy but my one question to you is... Do you do your exercises at home as well? It's all well and good to see a PT person once or twice a week, or even daily but you should be doing these exercises at home. It's hard work but you can regain some of the strength back. I visited PT twice a week. They gave me a set of exercises I could do at home too. So whenever I walked my dog I did them as I walked (minimum 2x daily) Maintenance is the key here. It's like being an athlete. Stop training everything goes to pot.
Now you've had radiation to that area I am sure so chances are the muscle memory is damaged. So you may have to do this daily forever. (use it or lose it... Right?) But over time you should see some improvement. It is a slow process but have faith.
Re the pain and swelling. Sometimes they go hand in hand. Swollen tissues can be sensitive and likely the fluid build up is pushing on healing areas. I was quite numb from my neck dissection - but I was also very swollen.
If you've had a clear scan (ONLY if you've had a clear scan) consider going to see a lymphatic masseuse. I waited until I was clear and then went for about 3 months 2x weekly. I did an abbreviated massage routine at home - these days my neck is really surprisingly good. I am still numb in certain areas (nerves have a very slow healing capacity and poor memory) but my neck looks normal and most importantly feels normal. Occasionally, I still feel a little swollen (often how I sleep is related to this) when I do I perform my abbreviated massage (takes a minute or two) and it goes away. It all depends on how you were rewired on the inside, but the massage even helps my tongue if its a bit swollen (go figure)
Radiation damages muscles it also impairs blood flow. My neck used to be as hard as a board. This is because my muscles had lost their elasticity from the surgery and rads. I underwent about 8 months of weekly acupuncture to my neck and we would rejoice when he drew blood. This means blood flow returned to the area. Without blood flow the muscle dies. Now my neck is soft and supple and about 99 % back to normal.
Finally ear pain.
Okay this is a tough one but with the surgeries you've had you've no doubt been rewired as well. I am not sure if you are on liquids and eating but I found that for a while after - because I was swallowing on one side (away from my damaged tongue) - I was getting fluid in my ear - it still happens some times. This would cause an earache as I think my inner ear canal would fill up. All these little holes in our head are connected. OR it could simply be residual pain from the surgeries you've had.

Despite the length of time from when you've been radiated to now you probably haven't healed completely from your radiation. I know it sounds strange but rads has long lasting and often a permanent impact on the area it is aimed at. So healing is an ongoing long term repair project. Kind of like osteonecrosis of the jaw. Why does it happen sometimes years out? Life cycle of a bone cell.. 25 years. Damage it... it's long term.

Hugs - and hope this helps a little.