1 - so it works error-free with IE9, as you requested ?
3 - Your first question :
if it works, leave it as it is, but this is nevertheless a good question
4- Your second question.
The answer is in my previous reply :
This one single js file could be divided into three (3) parts:
+ a compatibility layer for Mootools 1.12, developed specifically for Joomla (and not by me).
5 - Your last question.
You have to understand the logic behind Mootools. It is a modular framework. It means that, except core functions, you can pick up some (useful to your development) functions and leave aside others. I guess that is why Joomla Devs included the Mootools Uncompressed file in Mtupgrade. To help savvy JS developers work on this. And re-compress the file, thus lightening its weight.
You can also develop your own (Mootools) classes.
If you are interested in this topic, best is to read this article which presents a rather detailed explanation on Mootools (and the differences with jQuery) : http://jqueryvsmootools.com/
Hope it helps.