If you run the game, it should output the list of mods it's running with into the logfile - something like:
43331 [Thread-4] INFO com.fs.starfarer.StarfarerLauncher - Running with the following mods (in order of priority):
43331 [Thread-4] INFO com.fs.starfarer.StarfarerLauncher - $$Rebalanced Pilums [id: $$rebalanced_pilums] [version 1.1] (from C:\workspace\starfarer\mods\Rebalanced Pilums)
43332 [Thread-4] INFO com.fs.starfarer.StarfarerLauncher - $tarsector+ [id: dr_ssp] [version 3.7.0] (from C:\workspace\starfarer\mods\Starsector Plus)
43332 [Thread-4] INFO com.fs.starfarer.StarfarerLauncher - Galatia Complete [id: GalatiaC] [version 1.4] (from C:\workspace\starfarer\mods\Galatia Complete)
43354 [Thread-4] INFO com.fs.starfarer.StarfarerLauncher - Mod list finished
Might be easier to delete the log first, so that this list is near the top.
Also: what's the actual error message you get while saving?
And thanks for the heads up about the .baks. I've used them pretty extensively, but still use save copy to save from having to copy and rename files over and over.
Ah, gotcha, that makes sense.