Linux

1) I'm not sure what tools there are that will run on a Windows box natively for testing Linux security configurations. There's a whole bunch of stuff for Linux, though, and you should be able to run some of that from within Cygwin, which you can install on a Windows machine to emulate a Linux shell environment.

2) Dir command? Are you talking about using ls to get the contents of the current working directory?

3) If a shell command's output scrolls off the top of the screen, you can do one of two things to make it easier to view:

a. Pipe it through less, using the "pipe" (vertical bar, or |, on the keyboard) character. Thus, to pipe rpm -qa through less, you'd enter rpm -qa | less. You can then use the arrow keys to move up and down one line at a time, or use Ctrl-D and Ctrl-U to move down or up (respectively) half a screen at a time. There's more you can do, but that's the important stuff. To end the use of less (what we call a "pager" program), hit the Q key.

b. Redirect the output of your command to a file. You use the greater-than symbol to do this, and specify a filename to which the data should be saved. For instance, if you want to save the data in a file called rpmoutput.txt, you'd enter rpm -qa > rpmoutput.txt. Make sure you don't name it the same as something else you want to keep, because it will overwrite another file with the same name. Filenames are case-sensitive, though, so foo.txt is not the same as foo.TXT or Foo.txt. Of course, foo.txt isn't the same as foo, either, and unlike Windows your computer doesn't usually care what the file extension is: that's just to help you remember what type of file you're using. Then, of course, you need to read your file -- which can be done with less, like so: less rpmoutput.txt.

5) Two other ways to "manually" start these servers have already been mentioned by jmgarvin and Jaqui. Another option is to navigate to /etc/init.d and see if the services are there. If they are, you can start them with commands like ./httpd start and ./mysqld start. Of course, that ./ has to be at the beginning of it if you want to use relative paths and are inside that directory. You could also specify the full, absolute path, like so: /etc/init.d/httpd start and /etc/init.d/mysqld start. If they're already running and you want to restart them, you should be able to do so by substituting restart for start in the command syntax. If you just want to stop them, use stop instead. To check on whether they're already running, you can use ps ax to get a list of running processes (or ps aux if you want more information about each running process). If you want to know whether they're automatically starting when you boot the machine, you can use ls in the rc5.d directory, like so: ls /etc/rc5.d (assuming your system is running at runlevel 5 -- to find out what runlevel you're in, just enter runlevel at the shell prompt, then you can substitute the runlevel number for the number 5 in rc5.d).

Aside from the fact that yum is sometimes a problem (at least for my tastes), there's no particular reason setting this up with Fedora should be any more difficult than most other distributions. I tend to find everything easier on Debian, but I think jmgarvin would disagree on that score. Either way, it's generally the case that everything gets easy once you get familiarized with the basic unix way of doing things and, to some degree, your specific distribution's way of doing things. Good luck with all of that, and don't be shy about asking for help. Most of us who are fairly conversant in the workings of Linux are quite willing to share your knowledge and experience.