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

There is a free extension for adding canonicals - http://www.fmeaddons.com/magento/seo-canonical-url-extension.html - this does handle the parameter issue very well

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]