As my colleague has indicated, you need to consult with an attorney who specializes in litigating copyright infringement matters ASAP. There are a number of details that will need to be discussed in private (v. here on Avvo) and, as it seems you are aware, you are going to be up against a number of hurdles.
Most notably, pursuant to § 507 of the Copyright Act: "No civil action shall be maintained under the provisions of this title unless it is commenced within three years after the claim accrued." So, a big question will be when the claim accrued. While you have indicated that you just became aware of your materials being used in the second half of the course, a court will need to be convinced that you did not know OR HAVE REASON TO KNOW about that infringement until recently.
You will not be able to sue anyone for copyright infringement unless/until you have registered your materials with the U.S. Copyright Office. And, on a related note, do you own and control all rights in your materials even though they were created for a course at the institute? If you have a contract with the institute, what did that contract say, if anything, about the school's right to use your teaching materials in classes taught by others?
Last, but not least, if the school is a non-profit institution, you will need to PROVE that, pursuant to the relevant provisions of the Copyright Act, the school rather than the infringing instructor can be held accountable for the instructor's use of your materials.
Good luck to you.
Any answer or other information posted above is general in nature and is not intended, nor should it be construed, as legal advice. This posting does not create an attorney-client relationship between you and the posting attorney, and you are urged to engage a qualified attorney who is licensed to practice in the relevant jurisdiction.
Consult with a copyright infringement attorney to go over the specific facts of your case, but based on the information provided you should still be able to sue. The statute of limitations does not begin until you find out about the infringement.
The first question is whether you just found out that the second half of your course was copied back in 2006? Or was the second half of your course just copied?
The statute of limitations for copyright cases is generally three years, meaning that you can probably only sue for damages for infringement that occurred within the last three years. As to whether the three years starts to run from when you learned of the infringement or should have learned of it, that question is up in the air, and is interpreted a little differently in different districts.
You should sit down with an actual copyright attorney and talk through these issues. The threshold question will be whether you *should have known* about the infringement that occurred back then.