I launched my site using the pre-existing subdirectroy install and all but 3 pages worked great. Those 3 pages gave me the 'Too many redirects' error. After an hour or two of trying many things, I went to my server manager and we looked at the error logs. All the errors were 301 errors.
I realized that these 3 pages had names too similar to the old pages: the redirect was /rooms/index.php to /rooms/. I took out the line of 301 code for each page, made sure the old pages were deleted from the server and the 3 new pages now work just fine.
Hope this helps some people.