Thanks for all of the feedback! I think I'm covered as to my main questions about the location of the rail stations.

Additionally, based on these responses, we've decided to just pay as was we go rather that use the JR pass. That way we can use whatever transit line makes the most sense, rather than feeling like we need to use certain routes simply to make the pass more worthwhile. Plus, allows us to do the Nozomi and possibly green car if we feel like it. That extra flexibility is probably worth eating any potential savings from the JR pass...

Flight from HND on 13NOV is around 8:30am, so we really need to be in Tokyo the night before, rather than stay an extra night in Osaka.

Thanks again! This has all been very helpful.
KOB