You may not be able to use a tool like that to "fix" your pages. Simple things like a </td> (closing a table data tag) missing will make a page look totally different in IE vs FF. Adding it back can get the same result.
You might post the validation results. Also, you can post a link to the problem pages. It helps to see the page and view the source from there when trying to help on something like this. Maybe post a link to a page that has some validation errors but not the page that has the MOST errors
