.exe files are not supported, nor listed in the possible file extension choices. If you go to the configuration area of your site and click on "Security" in the left hand panel, then scroll to the bottom of the center section, you will see "Supported Files". You have the opportunity to select from a large list of file types; .exe isn't one of them.
You are correct, it does not have a "comment" option, but it does have "Ask a question". When clicked, it opens another page and gives you a check box option for "Discussion Topic" which may work for you instead of comments.
A couple ways to approach this may be to break them down into sub categories, using less numbers than 10. The alternate method would be to us "01-09" instead of "1-9". Unless there is a plan to go over 100, then it may be an option to use "001". Once the guides are created and are being assigned to courses, the numbering will really help.
Yes. There is a way. In the guide where you have the tool listed, open it up in view mode (not edit). Next to the tool listed is a button labeled, "View". Click on that button and it will open the WIKI where the tool is located. At the top right, select "Edit" allowing one to add a photo.
Is it possible to select user names that are already in the system to add them to a team, rather than send an email invite?