"One question I have in relation to the upper manifold gasket when I come to refit the manifold. Does the gasket go on clean or am I meant to apply some form of gasket sealant as well?"
I believe Page 12 of Ford's Racing Installation Instruction Manual says yes. This is an all Aluminium 427 motor but should apply to your case.
http://fordracingparts.com/download/...427AFT_ART.pdf