I noticed that you've not yet received a response. When stuff like that happens, with all those steps, it's hard for us who cannot see what you did or your files or setup to know exactly what to advise.
Did you resolve your issue? If so can you share what the problem ended up being and what the solution was? I know others would probably be interested as well.
If not resolved, from what I can tell this started with 404s, right? If that's the case, if there was a default .htaccess that really didn't need to be modified (unless you had modified it previously).
Whenever there is a URL change, 404s are common as the search engines figure out that the old URL no longer exists.
There is a great redirection plugin you can use that allows you to redirect each 404 to the most appropriate page on the new URL without having to touch any core files and offer the most user friendly experience possible. Maybe check that out?
Judith "Many of life's failures are people who did not realize how close they were to success when they gave up." ~Thomas Edison