Hey there :-)
Yes, it is possible to change the order of skills. You just have to change the parent IDs in the skilltypes.xml. My advice, before you change anything here, is to delete all characters before you restart a server with this kind of modded skills.
If you want to arrange a complete new placement of the skills, it will be more difficult. That would be interface stuff.
Someone who is familiar with torquescripting and interfacedesign will be maybe able to do things like this.
What do you mean with Realm-System?
The diplomacy-system of claims and guilds?