When you sign your PDF, do you specify 'Lock after Signing' in 'Sign document' dialogue box. As that would lock the PDF down and restrict you from making any changes.
Alternatively if you draw a signature field before hand, make sure in the signature field properties, under the 'Signed' tab is set to 'Nothing happens when signed', this will prevent it from being locked down.
Just to check, when you say 'Document Assembly' do you mean extracting pages, as the above method allows this but is there other things that you are trying to achieve.
Hope this helps?