The command varies from server plugin to server plugin cause some people make they're one plugins
You drag it into the plugins folder. If you want plugins in your minecraft server use bukkit, not the vanilla minecraft server.
No minecraft plugins will not give you a virus if they are from a high quality source
Yes. It doesn't matter if it's LAN I believe. You just have to download some plugins and put it in the plugins server if you're using vanilla minecraft.
Install bukkit
No, Minecraft Realms are 100% vanilla as they are provided by Mojang.
That depends if your minecraft server is vanilla, or with plugins, if it is with plugins like PermissionsEX then yo.u have to add the 'modifyworld' permission to the users permissions
To answer a faction invite just do /f join <faction name>
You use /f leave [faction name]
Because normal minecraft doesn't contain a faction plugin/addition without the use of modifications, I would suggest you find the name of the plugin for further help. As different plugins have different commands, we need the exact name in order to help you further.
I assume you're talking about a faction invite. the command is /f join <faction>
If you are in a faction, and want to teleport to your faction home, just type /f home.