Sounds like you have several problems. The big koi sounds like a bacterial infection because of colour change, the smaller one sounds like dropsy or possibly ick. Three weeks is time enough for many different diseases to build up and you got the jackpot. I always quarentine for three to four weeks before adding new fish to the pond. Here is a good website to look up symptoms and diseases, hope it helps.
http://www.bristol-aquarists.org.uk/...o/diseases.htm