Walk me through your steps? This is what I'd do, but I haven't actually tried it with other mods:

1) Get all the mods I want installed, but not activated.
2) Copy all of the files (in Public and Mods) from all those mods into a single mod's folder structure, the "empty mod" that Rhidian shared and described.
3) Activate that one compiled mod in the game.
4) Start a new game, save it.
5) Take that game's LSB and swap it into my live game's save folder, renamed to replace the LSB there.

That's the theory... but I've had several theories about mod files and saves that didn't work for me. :\