Allot of you guys have been asking me about the Ebola challenge and I apologize for not answering but I was away for a bit. I hope to clarify (without spoiling the challenge ofc) how I solved it. You might be working it out from a different angle and if that is the case I’m sorry but this won’t really help.
First off…I would suggest (and I think this applies to allot of crypto CTFs) to try the traditional encryption methods first (shift registers, substitution, play-fair etc). Since I want to avoid spoilers as best as possible I feel like if I say that the Ebola Challenge is based on a traditional cypher scheme most of you will get it. Wise words from @alamot at get stuck on Ebola - Challenges - Hack The Box :: Forums 
Personally I ignored the key.txt file, and resorted to handcraft my own python based script to help me decode the encrypted file. The book Cracking codes with Python is a great reference for any crypto challenge where you are using python. Hence I leave you a link to the book below .
This is not a how-to guide but a brief overview of the process I went through. This is the way I did it and you might have a different approach. Therefore I encourage everyone to try it out their own way before they tether themselves to one method or though process.
Good Luck
n3m0