Looks like you've got a lot of local support for routing, so I can't add much. But your post brings up the best memories I have of our 2008 TransAm. Well, except for the heat... and the flooding...

My wife and I branched off in Chester, rode up River Rd on the Illinois side to St. Louis, and eventually continued on up to Hartford via the Chain of Rocks Bridge. Hartford is where the Lewis and Clark Trail starts, which took us onto the Katy Trail. We crossed the Illinois/Mississippi Rivers on the Grafton ferry, looping down to St. Charles. If I was gonna do it again, I wouldn't change a thing -- even though there are shorter routes from St. Louis to the Katy.

Edit: Well, we tried to take the Grafton ferry; it was closed due to high water. Instead, we took the Brussels ferry (free state ferry) to Calhoun County, and then the Golden Eagle (private, $3 per bike) across the Mississippi into Missouri. This is actually the route the L&C Trail takes, and worth the extra miles for the beauty of Calhoun County.

Our three days on the Katy were cycling heaven. In my mind, you couldn't choose a better way to cross Missouri and into the Kansas plains. Taking the extra miles from St. Louis to the Confluence (rather than direct to St. Charles) was a history lesson in itself, a river and ferry adventure, and prolonged the introduction we had to the heartbeat of the Midwest. If you have the extra time (only a day or two), and the legs, I'd recommend it.

The only reservations I'd have about diverting from the TransAm to the Katy Trail would be adverse weather conditions. The trail is crushed limestone, so it doesn't really turn into "mud". But a wet spring, or a lingering hurricane in late summer (as in 2008) could make it a marathon ordeal of submerged hubs and dodging fallen limbs.

Our ride was 2 1/2 years ago, but I don't expect the experience would be much different now. Here's a link to the start of our three days on the Katy Trail.

-- Mark