I've been validating my site on http://validator.w3.org so far so good but what I'm interested in is validating my page that has been modified by Ajax requests. Viewing the source code afterwards wont show the new code in Firefox and its the same for other browsers I believe(yes I have tried and cant remember ever seeing the newly inserted HTML in the source code).

I'm certain my code is not going to be valid there because I've hacked away at getting it to work and its very long so there are bound to be mistakes hence the reason why I would want to validate it. Are there any methods for checking it beside the obvious copy and paste each section of the Ajax request responses in to the direct input textarea provided by W3. Its going to be very tedious this way and if thats the only way I do not think I will bother just yet. At-least it works right and no one will ever see the source code unless they have the PHP files.

You can't see the manipulated code after AJAX calls as the browsers make changes to the Document Object Model and render the changes. I'm not sure but DOM viewers might help you. Free DOM viewers are available for both IE & Firefox.