Congrats on joining the "Insight club" with your purchase! Overall, I don't think you're missing anything critical from the prior owner. Here are my thoughts on your questions/list:
1. The Owners Manual and Navigation Manual aren't included at delivery, but as you've seen in other threads, they're available free to new owners within the first 6 months of purchase. Wondering if you might have difficulty ordering a free set, since you're the second owner (?).
2. Not sure what the plastic black plugs are; would be interested in seeing pictures. The only thing that comes to mind are "wheel well fasteners" mentioned in this thread
, or possibly carpet hold-down fasteners from the rear of car (see #3).
3. The screwdriver might be the "bonus" one that's typically missing
. Do you notice any modifications or add-on accessories, which might have been added with these extra tools (e.g. cargo hooks, cargo net, LED rear turn lights)?
4. Your cupholder set-up sounds ALMOST complete to me. The Touring model should have a coin tray that the LX/EX doesn't have, discussed here
and looks like this
. Part can be ordered here
, but it'd be better if the dealer made you whole.
5. The phone mount and cable guide are definitely not OEM.
6. The key number tag is worth follow-up, to make things easier in the future. My tag is thin, white plastic with a printed bar code, and 4 character ID below the bar code.