I would say unless everything was photocopied you are screwed and will need to do the cross country's again and get the signatures requred.
As for the FRTOL and ground exams forms I am sure that your school would be able to fill out some more forms with the "correct" signature.
One good thing (but not good for you) is the CAA are asking the school to explain themselves, and I would imagine it needs to be a bloody explanation in order to prevent the CAA taking action.
When you say you are sure the missing items were included...how sure are you? did you personaly check everything, seal and send the envelope yourself?