I have been working on a contract basis for the past three years with a company that I used to work for as a graphic designer and photographer. Over the past 7 years of working with them as an employee and now owning my own business I have created a group of product and event photos of about 3000 photos of which half are since I had left as an employee. All of the photos where shot with my camera and their lights. When I started my own business, they leased the lights to me for $1.00 per year and we have a contract drawn up for that which lists the equipment.
They use these photos (mostly product photos) for all of their marketing: brochures, catalogs, press releases, website and anything else that they might think of. I am the one who also designs most of these things. They pay me according to a contract renegotiated yearly by a specified number of hours per month with all hours at the same rate weather graphic design, photography or whatever. There have never been any licensing terms or copyright talked about or listed in print in any contract. I know this is foolish, even if he did say, "We don't need a contract, I trust you".
Recently, he asked me who I believed owned the copyright to the photographs. I replied, "you own the copyright to the ones that I took when I worked for you and I own the copyright to the ones that I took since I left." He had been assuming that he owned everything which I did know he would assume this from working with him for 10 years. I get the idea that he is planning to take all of the photos as his own and tell me he has found someone "more economical" so he can save money in rough times.
The reason that I had never pushed any licensing is that I was doing all of the design with the photos that I had taken so why complicate things. We're family, right.

I know better now.
Finally, my questions for now, I think, are:
1.)In light of these circumstances, am I correct? Do I own the copyright on these images?
2.) Can I now submit them to be copyright office now after some have been published over 2 years ago?