Hi there!
Looking at your itinerary, I do think that a 14 day JR pass would be a great help, both in terms of savings over normal rail prices and in convenience. Looking at savings, you would be sure to make some nice savings, especially with all your planned day trips. The JR Pass would absolutely cover all your train travel to these places. As for convenience, you buy one ticket for all your travel meaning that you won't have to buy tickets every time you travel and it also makes for very easy budgeting.
Now let's have a look at the JR Pass vs Night Buses. It is hard to make an exact price comparison as night bus rates change by the day. Given that I do think that you would spend (slightly) less money if you used night buses for your major travel instead of the train, especially since you can save on accommodation costs as well. Personally I would take the train over any night bus. Simply because it is hard to sleep in them, you can't look outside because curtains are everywhere and you pretty much loose the next day due to fatigue. This is not what you want when your time is limited in Japan and want to make the most of your trip. Also trains are much more comfortable and you have to ride the Shinkansen at least once when you visit Japan.
Anyway that is what I think, let me know your thoughts!
-Daniel
PS: You are kinda asking the wrong forum if you want a positive review of night buses, this is the JRP Forum after all :)