The fluid being a little over the full mark shouldn't hurt. Just like the oil, they have some tolerances built in to allow for slight over-fills.

Since the odometer dies when the O/D flashes, I'd assume some kind of electrical gremlin versus a tranny problem. That leads to a long time consuming list of possibilities. Some shared fuse, wire, ground, etc that could cause the problem. I know some of the earlier Escapes had an issue with water leaking around the windshield and causing rust/corrosion around the fuse box.

You said it shifts choppy until it warms up. Choppy as in - more than in the past? Or choppy as in - more than the vehicle you drive daily?