Depending on what direction you are headed, I would think you could handle the NT if going west bound. There are a few noteworthy hills in New England then relatively flat until Glacier National Park in Montana. From there, you get the typical western Rocky topography, i.e. long ups and downs. If going westbound, you should be in pretty strong shape by then but you will have battled some headwinds during the trek. I did this east bound and only thought western OR and Glacier were the more difficult areas. Perhaps you could do a "warm up" tour on the San Juan Islands before heading east???
The TransAm is a great route (my favorite ACA route). However, this route has more sections of noteworthy hills. I personally think the Ozarks are harder than the Rockies since the hills tend to go over versus around the hills. The Rockies are overall pretty steady slopes whether going up or down. Then eastern KY/Western Va is at times a bit of a struggle. The Rockies in Colorado really aren't that much trouble but the altitude might slow you down.
I have not done the Southern Tier (I plan on doing 1/3 this spring). The entire eastern half (Austin, TX east) is flat.
I would suggest you look at several journals over on CrazyGuy to see what you think. I would also suggest that if you did the Atlantic Coast route without difficulty, you would most likely be fine on any of the route IF you were in shape prior to starting.
No matter which route you choose, hope you have a great trip!