Thanks for the detailed answer fireundubh, I'll give it a try. Good idea with junction points, I didn't think about them.
Out of curiosity, do you use version control or do you simply zip the files and upload to dropbox (or other solution)?
I don't use version control for my mods, but I have the game data, editor data, and patch data in local Git repos so I can see what changes between patches. I don't use Git for my current mods because I wrote Python scripts to automatically generate the largest ones, which makes them too simple for a commit history to be helpful.
