Wow, I had quite the little pity-party going on for myself yesterday. 
Len, thank you so much for all your advice.
The last day I ran was last Wednesday. My neck felt okay during the run, but was incredibly sore after the run for about 2 days, which is when I no way could run in reasonble comfort. I could barely turn it and would not be able to deal with all that head-bopping and joggling a run would create.
I've been doing neck stretches and taking a bit of ibuprofen, and today my neck feels pretty good. My husband and I are going on a 1-mile run later and he said he'd observe my running posture but he's never noticed me running with my shoulders up. I told him that on my run with the big water bottle, I myself discovered my shoulders up and had to slow down and roll them back a few times - I don't know if it was the heat, the length of the run or the water bottle that caused me to tense up like that. If today's run goes well, I'll test the waters again on Wednesday with a 4.5 mile run and if that goes okay, maybe I can finally get to that 9-mile run on Friday.
My race is less than 2 weeks away and I don't know what to do for that final week. The Hal Higdon program has a couple of short runs that week, but since I haven't run any long, long runs, should I try to get one more in if my neck cooperates? (If my neck doesn't cooperate, I'm still running the half-marathon, and I'll just deal with the sore neck later.)
I like your idea of heat before a run. Thank you.
My thoughts on your sore right shoulder - it's possibly caused by reaching for your mouse. My desk has an under-desk adjustable keyboard/mouse tray that practically sits on my lap and my mouse is near my right hip. I know that doesn't work with a laptop, but maybe you could keep your mouse closer to your body.