Brian, I'm glad you asked about the High ISO NR, as I hadn't thought much about it since buying my 5DIII almost two years ago. Rather than summarizing an excellent article on the subject, I'd refer you to this post on Canon USA's website: http://www.learn.usa.canon.com/resources/articles/2011/high_iso_noise_reduction_article.shtml
The key word in this article might be "experiment."
As for question number two, I'd be very interested to hear what some of the more engineering-minded regulars of CR have to say, but from my own experience, in the lower ISO values (400 and below), factors like wind or the steps of a passerby or the passing of something in front of the field of view are much more important than a little difference in noise. That said, even a normal exposure (eg 1/200th) is going to reveal a little more noise at ISO 400 than at ISO 100, so starting out lower seems pretty sensible when possible. But you do raise a good question about length of sensor operation effecting noise more than ISO value.
But if you are seeing "very noisy" at ISO 100, I wonder if you are trying to boost the shadows too much in post processing?
Question 3...The longest lens I have with IS is the 70-200mm 2.8 II. In my experience, turning IS off on the tripod is a must, no matter how long my exposure. Page 10 of the user manual suggests turning IS off for long exposures, otherwise "the stabilizer function may introduce errors." From my undertstanding, I don't think IS gives any real benefit once the shutter speed is below 1/15th of a second or so for a still shot.
Question 4 is probably another candidate for experimenting, especially with Milky Way type shots, but page 145 of the 5DIII manual, referring to Long Exposure NR, does state: "Images taken at ISO 1600 or higher may look grainier with the [Enable] setting than with the [Disable] and [Auto] settings."
This seems to be suggesting a ballpark answer.
I'm going to go back and experiment more with High ISO NR. I've had very good luck with cityscapes at night with Long Exposure NR, but I turned off High ISO NR two years ago and left it off, depending on Lightroom and sometimes Photoshop to deal with noise.
Here's a link, also to Canon USA, that puts a lot of nighttime exposure advice in one place, with a good reminder about mirror lockup: http://www.learn.usa.canon.com/resources/articles/2012/long_exposure_landscapes.shtml
Also explains Long Exposure NR a bit.