You can copy all your FCE projects and media assets. I don't know what you mean by "FCE Assets". If you mean your project files and all the files/folders in the Final Cut Express Documents folder and child folders they are your media assets (including the clips, cache & render files and other stuff in those folders). Those folders & files do not contain anything that is subject to the FCE license. You can copy them at will.
The only thing that is subject to the FCE license is the FCE application itself.
I think you are on the right track to have a double-backup (what you called a third HD). Note, also that there is no reason to copy any render files, cache files or waveform files. They are temporary files and you can always re-create them by opening your FCE project file and re-rendering. For what it's worth, copies of render files are practically useless; they just take up disk space.