Ok, one more thing. At hyperdia you can tell that a train is a JR train if the name starts with "JR" or "LTD EXP" or "SHINKANSEN".

The Kintetsu, Hankyu, subway, and others are not JR trains and not covered by the JR Pass.

Thank you for the comprehensive "JR Rail 101". Such valuable information. Now I can decipher most of what I read on hyperdia. Appreciate the amount of time you spent in writing your post. I hope others on this board who are looking for similar information will find it useful too.
The Japan Guide link is very useful. Read up on the Toyota plant tour in great detail.
Understand that there is no onsen in Kyoto! Oh well, already too much on the plate. Save it for another trip perhaps.
Yes, I found the pdf files (from link you provided describing various destinations and practice guides) extremely helpful. In days to come, I will be download them and put them to good use in my planning process.
As usual, appreciate your sharing your travel experience. Have a good day!

Good. I should clarify: I have read that there are sento (public baths) in Kyoto, just would not be hot springs water.