1.) I don't think that would be a problem since your friend would be getting a copy of the cover letter with the 'Received' stamp on it, which would be handed over to you eventually.
2.) You can submit your application anytime between 9-5PM (Mon-Fri).
3.) Hand it over to the front desk. They forward it to the Licensing section.
4.) Yes
P.S. - Make sure you keep photocopies of every single document you submit to the DGCA. They are bound to misplace the originals.