We attempted to install sh404SEF AFTER the site was set up, operational, and we had been using the "redirect" plugin.
It absolutely DID NOT integrate well at all. None of the already programmed redirected urls worked...and there were just too many 404 pages coming up to be dealt with.
This program is one of those things "I wish I had installed before creating the rest of my website" because maybe then it would have worked...but as it stands, it does NOTHING for our site and we have uninstalled it completely.
Sorry for your bad experience. Indeed, installing ANY SEF extension after your site has launched and has been crawled by search engines requires some work.
Namely, those urls that are modified by the new extensions needs to be redirected to new ones.
That can be done either in a .htaccess file, or using sh404SEF built in redirection management.
However, I can already tell that from next version, sh404SEF will also check Joomla! own redirect manager database table in case some redirects have been stored there previously
Thanks and regards