Ok, I think I see what you are trying to do. For a direct answer, no, I don't see how you can apply a content type directly to a document after it has been placed in the library. However, it sounds as if what you want to do is attach the metadata from a content type to a specific document. If you think of a content type as nothing more than enforced metadata structure, you can work your way around this.
First, add all of the metadata fields to your column list. Then, create a view that shows those metadata fields, change to datasheet view and add the metadata for those documents. I've done this hundreds of times for data in a multi-media library. Because you are in datasheet view, you can cut and paste, drag and fill, all the basic stuff from Excel. It's very efficient when you've got default values for the fields that can be filled in quickly.
I hope that helps. It's good that you are trying to preserve your metadata since this will be a major part of your search infrastructure once you get setup.
Regards,
Mark
EndUserSharePoint.com