Oh yes, it is definitely not fun to get that confirming diagnosis. The only good thing is now you are done with that stage and can start to do something about treating it.
I don't know why there would be such a difference in size but I bet there is some explanation for that. Maybe the physical mass is 7x7 but only 3x3 of that mass is actively high metabolism. Only the high metabolism part will 'light up' on the PET scan. For me the sizes matched which meant the whole mass was active. I am just guessing, your oncologist will have to explain what is really going on. That is good that it has not spread too far. My lung mass was also lower right lobe but the PET scan showed I had a high metabolism mass in my right sinus, of all places. They had to remove that surgically and found it was not cancer, just some high metabolism mass growing there. Good to have it gone anyhow.
If the lymph nodes are all the very nearby Hilar nodes that is a little better but if some are the little further away Mediastinal nodes then that moves up the stage rating like from 2 to 3. Again that will have to come from your oncologist. Mine was stage 3B because I had both lymph node locations.
The sore throat from the biopsy sounds just like my experience, sore for several days but slowly fading away.
I'm very sorry to hear you are having constant pain and I wish your appointment was sooner to address that issue. I didn't have that. Could you see your regular doctor sooner?