Welcome to the ACA Forums!
It is a bit hard to give some detailed recommendations. Try looking at this:
https://forums.adventurecycling.org/index.php?topic=14587.0 for some suggested questions to answer. Other things to consider for your specific trip is do you want to tour in your area, an area you are not familiar with (what states??), what temps do you prefer (be specific in degrees not vague like "cool"), etc. Just give your "must haves" and your "preferreds".
As far as the e-bike goes, you might be able to do a tour with an e-bike but I would wonder how many times you will be riding unassisted because the batteries died and you have no where to charge. If you are hoteling it each night, then that is a different story. A used regular touring bike, a la a Surly Long Hall Trucker, might be worthy considering. You could then sale it after you get done and the overall cost would be fairly low.
September and October are great months to travel typically. Without knowing your answers, I would probably start with ACA's Atlanta Coast Route (AC)and head south. I personally do not like parts of the East Greenway as they can have tremendous traffic and times. ACA reserches their routes much better IMO. Anyway, take the AC to the Chicago to NYC route (CNYC) and head toward Indianapolis. From there, follow the East TransAm Express route (non-ACA) to St. Louis where you can take the train back home. If you have more time, you can pick up the Katy Trail, a rail trail, in St. Louis, and end in Kansas City (take train back).
Of course, a great area is New England and its colors, i.e. MA, ME, NH, VT, NY then head down to Pittsburgh and circle back to MA using the CNYC and the AC back toward home.
Due to the time you are traveling, other than the northern Rockies, you can almost travel anywhere.
Tailwinds, John