I have 2 questions: 1) What did the kois died of? One thing I feel I must
add is that the filter was clogged when I found them)

Chlorine probably.

Put the fish in a container of the water from their pond, then clean
the pond. Fill, and then put de-chlorinator in the newly filled pond,
and then put the fish back in when the time is up for the
de-chlorinator's purpose. The bottle will tell you when it has done
its job.