Since the flooding, parts of the Confluence Trail is in a bit of a state, with the road covered in brickabrack left by the floodwaters, just south of the Great Rivers Research & Education Center Field Station (what a mouthfull). I don't know when they'll get around to cleaning it up. Once you get past the Lewis & Clark Historical Site, Camp River Dubois, the trail goes from asphalt MUP to crushed gravel Levee road. I don't know how the trail is from there. The entire trail from Alton to Hartford is mined with Goose-droppings! There are also roving gangs of wild turkeys near Hartford.

Rather than staying on the Confluence Trail through the East St. Louis area, I'd cross the Old Chain of Rocks Bridge, and use the Riverfront Trail, though the gain in safety is probably marginal at best. Daylight hours, and don't leave vehicles (including bicycles) parked unattended at the trail parking lots, and you should be no less unsafe than anywhere else in the Continental US...