_But there will be a lot of old files left that have no equal in the new site. Do I just delete these, or noindex nofollw them? _
If any of the old pages left benind have" Page Rank" ascribed to them, you might consider creating "catch all" pages on the new site so as to be able to 301 the leftover old to the new "catch all" pages and thereby reatain the link juice.
This requires creativity as you don't want to lose usability just to catch more link juice. Not knowing your exact situation I'm not positive this is an option but mention it just incase.
