I can't speak to the other stuff, but the application checklist is pretty clear that they want the marriage certificate. Not sure what you mean by original registration.
Looking at the new application kit with its dropboxes for country-specific stuff, if I put it in as you mentioned (Sweden as the country of residence, and then including Afghanistan as another country), it doesn't show a need for IMM 5562. Interesting. And potentially problematic if their little thing isn't telling people the right things to include and then the applications are getting returned based on that. Though regardless of that form, the marriage certificate still would have been a problem.