I am going to give this a try. Keep in mind, that I am just an advanced functional user, and my knowledge of networking is only what I have picked up over time.
Media Server and Web Remote are two separate items in MJ/MC. Media Server allows you to access a library on a "server" pc, and use those files on the "client" machine. Web Remote, allows you to control the "server" from a remote location. To further enhance the functionality of the Web Remote, a more enhanced version of the Web Remote was built by a MJ/MC user, called Glissando. I will get into setting that up later.
In terms of the ports, you can use whatever port you like, as long as that port is not being used by another piece of software, and that it follows the guidelines in the Install.txt file for Glissando. I beleive that states that you must use something higher than 1024. Ports are just an additional means of designating an "address", beyond the IP address. (sorry if I am incorrect in my explanation, but that is about all I know about ports) Anyway, if you use Media Server, and you use port 8080, then for Web Remote, you should use 8081, as you can not use the same port numbers of an IP Address for different software applications.
FQDN, is not a term that I am familiar with, but according to the install instructions for Glissando, you need to specify the IP Address of the "server" computer in the glissando.txt file. Again, follow the instructions in the Install.txt file.
Regarding JimH's comments about testing this from an IE browser session, I can only guess that he was telling you to type the IP address, with a colon, followed by the port number, hit enter, and see what comes up. If Page Not Found, then the Web Remote pluggin is not functioning properly.
Setting up Glissando, is fairly easy if you follow the Install.txt instructions. Let me know if this does not help, and I will try to get more specific.
Drew