Do you have any links to the before and after versions of the pages so that we have a reference for what has changed, screen shots may help as well. When you were using Theme It to make the changes what are the steps that you took?
In regards to the error you are getting when using the tool have you tried deleting the cache file to see if this helps to resolve the problem? Here is a link to the page with instructions for this to see if it can get you past this error. Please post back with the details and let us know if the error has gone away so we can determine how to proceed.