I had similar issues trying to upgrade my Win 8 Pro to 8.1. Initially, had an I/O error 0xc00000e9. Later, it was another (I didn't document it). Removed all connection but mouse & keyboard --same result -- Return to 8.0. Did a "repair" -- same. Did a "refresh" -- same. Lost a lot of saved email history when outlook was removed.
Then, on a "let's do something" lark, I disconnected & reconnected my 1 TB HDD. Voila!!! IT Worked. 8.1 installed without further problems.
Next task(s) is reinstalling all the programs that were removed during "refresh".
I hope this helps someone.