Historian,
Even though I have used the C&O Towpath inside the D.C. beltway as a running path for years, I have no particular information on the rest of the trip. I will only comment on two of your points.
a. "...and I need more experience to ride it." As long as you take the time to train before you depart on a cross country trip, you don't need any special additional experience. Just do it. I completed the Southern Tier solo unsupported with zero experience. On a road bike. With two panniers. And the trip was great.
b. I only tour with two panniers. It works fine.
Good luck and have a good ride.