SKSE version 1.7.3 and onward support a new diagnostic function that will inform you if your load order is missing a master, and will tell you specifically which mods are missing when the game tells you it's missing content from a save. This feature hasn't been widely publicized and it's extremely useful for finding these kinds of problems for folks who refuse to touch Wrye Bash for whatever reason.
In the [General] section of Data\SKSE\SKSE.ini (create the file if it doesn't exist there) you can add this: EnableDiagnostics=1
My file currently looks like this:
[General]
ClearInvalidRegistrations=1
EnableDiagnostics=1
[Memory]
DefaultHeapInitialAllocMB=768
ScrapHeapSizeMB=256
If all you want are the diagnostics, you don't need all the other stuff.
For a missing master, you'll see something like this:
For a save missing content, you'll see something like this: