add some clarifying language for beginners, fix bad link, correct typo

Hi guys,  

In addition to the edits below, I also wanted to mention:

1) At first I didn't realize that I should be typing the commands into my Git Bash terminal.  I could tell that the text in the gray boxes were commands, but I didn't know where to type them in  (complete newb here).  If you expect other complete newbs, it might be good to be explicit and say "Throughout this document, text in gray boxes should be entered into your Git Bash terminal"

2) When running modtool list (line 60 below), I didn't have the tools/bin set up in my path, so I was encountering issues with this.   Actually, I'm still encountering issues with this, even though tools/bin does show up when I do the 'echo PATH$' command... not sure what could be the issue.