Nexus 5: /storage/emulated/0 not mounted
OK, so I finally fixed this problem.
I wiped my phone completely after backing up my data and I used fastboot to flash an all new recovery image and installed a new ROM but still the problem persisted.
Then I noticed that in the recovery I keep getting: "error mounting /persist".
I found and followed this link: http://forum.xda-developers.com/google-nexus-5/general/guide-to-fix-persist-partition-t2821576 
And the problem was fixed!