I guess the best thing is that you feel you are improving. As for what questions you should ask and who you should see, I would be pushing for a 2nd opinion from another neurologist. I'd also be keen to see if they did an EMG on the paraspinal musculature at the C/T junction. A root lesion there will give atrophy here as well, it should be a routine part of an EMG exam when trying to eliminate a root lesion; however, it can be forgotten. A few more questions though:
1. When your neck painful you had to hold it forward, as in looking down improved your pain levels? This will open the IVF and give the nerve root more room to move and relieve some of the discomfort associated with it if there was some encroachment on it.
2. Also, were there positions you could put your arm in that improved the arm and shoulder pain (ie. holding your arm over your head)? I ask because these are findings common to a mechanical lesion in the neck involving a nerve root.
3. When you post when squatting at the gym did that aggravate your neck pain by chance or give you discomfort in the shoulder? This would increase the intrathecal pressure and aggravate a sketchy disc.
4. How long has this been going on for now?
5. When you say you can't get your whole pec to flex is it more the sternal fibres or the clavicular fibres?

As I said previously I'm surpirsed that an infectious or an autoimmune type condition like they propose only managed to affect one nerve root, although possible, I'd just want to be confident that nothing mechanical and more plausible wasn't missed. It's more likely to have an uncommon presentation of a common condition than to have an common presentation of an uncommon condition.... Diagnostic words to live by.
At any rate it's an interesting case and it would be great to view your films and read those EMG reports. Would be amazing if they could get posted somehow! Thanks for sharing, I hope you find this helpful.
W