Mr F
You are right that gore tex has improved a lot since the early days, and I am actually a big proponent of it for mountaineering apparel. I have never been sold on it for a running shoe however.
On a mountain hike I wear gore tex trousers, and gore tex gaiters to prevent the water getting in over the tops of my gore tex walking boots. Remove any one of these components and the whole system collapses. Once water gets in via the top of the footwear, it stays in. Even if water doesn't get into the footwear, the sweat will build up faster than your body heat can push it out.
I don't know the deal with the Thames 100, but I know that the NDW 100 (also a centurion event) gives you access to your drop bag at 25, 50 and 75 miles. This means that you can have multiple spare shoes and socks to hand. If you are bent upon having some protection from the water, then a pair of sealskin socks can be carried in your camel-back. They can be put on if required, and will be more resistant to ingress of water from the top than waterproof shoes.