I finally got the permalink problem fixed (knock on wood). Now on to the next big problem, broken RSS feed. now instead of sending back to the front page it's giving an error page. So when I went to feedburner to validate the site, it gave the error below:
This feed does not validate.
line 1, column 1: Blank line before XML declaration [help]
In addition, interoperability with the widest range of feed readers could be improved by implementing the following recommendation.
line 12, column 103: Self reference doesn't match document location [help]
... rel="self" type="application/rss+xml" />
I have looked through every .php file of the theme and non of them have this blank line above it. The header.php does have the DOCTYPE part, but it's the very first thing in the file.
Also the part on line 12, I haven't been able to find the code they mentioned. Any ideas would be great...