Jeff,
I'm glad you feel the seminar was beneficial. We try hard to pack lots of information into our allotted time, and it can be overwhelming.
Number 3 is the scenario that you would use. However, I would submit that, if you measured the course the first time, you should not have to re-measure. You still have all of your original paperwork from the measurement. That should suffice as the supporting paperwork for the new certificate, with a new Course Name, and a new certificate number. There is no stated time limit on how long can be allowed between a measurement, and the submission of paperwork for certification. Some measurers take months to get a certification package sent, if the race is not going to be run until the following year, for instance.
What I said in the seminar, and what is reiterated in the policy, is that we encourage courses that could be used by many, to be named for the venue, and not a race. Thus, the "City Park 5k" can be used by many events, and the map/certificate does not promote one charity over the other. It is awkward for Race for the Cure to use the Diabetes Dash 5k course, but if it is the "City Park 5k" course, there is no conflict.
Good luck in settling this. You will need to submit new paperwork (and the fee) with the new course name, whatever the course name turns out to be.