There are three steps to this

1. add no-index tag 

2. add canonical tags

3. Add them to robots.txt with disallow mark

Wait for few days for changes to implement
Ignore / mark the 404 errors as fixed

For change from .html to non html - You need to apply 301 redirection. here is code

# Rewrite valid requests on .html files  

RewriteCond %{REQUEST_FILENAME}.html -f  
RewriteRule ^ %{REQUEST_URI}.html?rw=1 [L,QSA]