Low space even though most apps are linked to SD card
This sounds a lot like an issue with cache. While the apps themselves can be stored on the SD card, cache that they produce might not. As I don't know what apps you actually have, I can only advise you to at least try and delete cache from various apps, such as twitter, facebook etc.

To delete cache, do as follows (this is for android 4.3): Settings -> More -> Application manager

Here you should be able to click in on every installed app, and delete their cache. Beware, tho, for something like calender and alarm clock apps, any set up serviced from them might reset! This should not, however, delete the app itself.