Depending on packing style you can easily carry enough. If you were to pack light two panniers each could be plenty. Even two front panniers each can work if packing very lightly.Good points made. I definitely don't want to be one of those "bring the kitchen sink" type of people. Still, there are some things that I think are worth adding to my long tour packing list. For instance, it's pretty easy to plan for weather on a short tour in the pacific northwest summer, but a 2 month trip across a range of climates would seem to require carrying gear for various contingencies (rain jacket, arm/knee warmers, etc.). It also seems prudent to carry a few maintenance-related items that I wouldn't bring on a shorter trip (portable cassette tool, pliers, spare tires). In addition, I gather that the western portion of the ST has some significant low/no service sections, so having space for more food and water seems like a good idea.
You really do not need to carry more for a tour that length than for a shorter one. I would suggest you consider taking only what you have been using so far on your short trips for your longer trip. Think about what you really need before deciding.
Some folks happily carry a ton of stuff. If you are in that camp feel free to ignore my comments. On the other hand, as I have gone lighter and lighter I have found the experience better and better.
I will say that September definitely wouldn't be my favorite time to be doing a Southern Tier. I would think you will experience very hot weather. February is prime time for starting this route in my opinion. It is nice and cool and the days are starting to get a bit longer, as compares to going in December. You couldn't pay me to do it in September, but I am a hot weather wimp and don't mind a bit of cold. Having done it a few times, the experience of riding in 100-110F in the desert is definitely an experience that I have no desire to repeat.
Still, it seems as if 6 panniers will be more than enough room to accommodate what we want to carry. I think I was more concerned about the handling characteristics of a rear-heavy load. But perhaps it's not worth worrying about.
In regards to departure time, I know that leaving from San Diego in late September will force us to contend with some hot weather in the early part of the trip. But it seems manageable and it fits best within our life schedule. We'll have to see how it goes, I guess.