I was driving by a restaurant, in my area, and noticed that one of my stock photos was being used on banners, and on the menus as a logo. It's a picture of Guava, and the name of the restaurant is "Guava". I asked the owner where he got the image, and he said that his designer found it on the internet. I informed him that I was the photographer, and he agreed that if indeed I was the photographer, he would be willing to pay a licensing fee. I have since sent him a contact sheet of the original photo shoot, along with photos of the layers of the stem and leaves used for the photoshop composite.
   He has now sent me an email stating that he received the prints, but still has not received any copyright documentation constituting ownership or the ability/right to sell the artwork. I'm stumped. How do I prove ownership?

I guess you could direct him to the page on IS (or wherever) which indicates that you are the copyright holder.

Surely his designer must have bought a license already (although I believe should be an EL for use as a logo)?

2. The image was not bought from a microstock site. It was taken from the online portfolio of samples, on my website.

Well surely, on your website, there must words to the effect that you own the copyright, etc? Maybe they thought your 'samples' were free to use as that term implies.

1. From the Google searches I've done,
Q. Do I have to file anything in Washington, D.C., in order to get a copyright?

A. No. A copyright is secured automatically when a work is created. This concept is frequently misunderstood. Some people still believe that there are formalities required in order to create a copyright. This is not true. Under the latest version of the Copyright Act, neither publication nor registration with the Copyright Office of the Library of Congress is required in order to secure full copyright protection. When a work is created, it is automatically copyrighted.

2. The image was not bought from a microstock site. It was taken from the online portfolio of samples, on my website.

You're correct, " Under the latest version of the Copyright Act, neither publication nor registration with the Copyright Office of the Library of Congress is required in order to secure full copyright protection. When a work is created, it is automatically copyrighted. " if you have the original file of that photo, you have every right to claim that you're the copyright holder, in that case I would contact an attorney and get paid for what's rightfully yours from the designer and or business, for using the photo without the copyright holder's authorization, using the photo for a business logo without the correct license (EL) and probably including  the attorneys fees, also try contacting the Better Business Bureau Dept.