Something isn't right? I'm afraid that you need to start al over - learn ADB and forget about those Toolkit(s) unless that are specific & updated for 4.4.3 compliance. Mine is a 2012 WiFi model with 32 GB, internal storage/total space is 27.58 GB and even with apps & pix, video, etc. on the SDcard, and Apps taking up space, I have 19.1GB available.
First, might I suggest that you upgrade/try the newest recovery - either CWM or TWRP (using 18.104.22.168 on mine) to install - doing a full wipe & factory reset is best way/recommended AND yes, time-consuming, but you get it "right" almost every time - wipe three (3) times each - dalvik cache, cache and factory reset/full wipe. Then, re-flash your factory rom/image file - be patient, as it will take 5 to 10 minutes for it to finish, take a break or whatever. When it's done & without error/abort message, reboot the device & let it settle for a little while after configuring WiFi as those download Apps and update could take a while if your mobile data plan is limited. Personally, I'm "biased" toward TWRP and I don't have to deal with MD5 check/error message that pop out of nowhere with CWM.
If everything works as planned, you will be shown the Setup Menu to configure - profit & enjoy, check the storage size (you can see what's taking up the space) then, restore your Google Account with the Apps, and reboot when finished.
Good luck & let us know your progress or results.