According to Link2SD I only have 2% system space left I have plenty of space everywhere else. How can I fix this?
System space is internal andoid space (not your SD card/storage space). To make more empty space available in your system, you can do the following:


Clean system cache (there are various apps to do that);
Uninstall unused apps;
Move apps to sd card (with App2SD or similar application);


System space depends on the device and is limited amount of space which contains your ROM, system and applications. It is not good if it has only 2% space left as your device might become slow or cause some apps to crash.