The Canal Tunnels part of TLP has yet to reach the drawing board. (Or tender phase!)
I actually visited St Pancras this morning, and have a fairly good idea of how the layout should look, once completed.
Blackfriars station as has been said previously, is going to completley change both in image, and layout. The Thameslink tracks will be slewed over to where the bay platforms are currently, and the lines from Elephant & Castle will terminate where the current Thameslink line is. Its effectivley turning the station layout on its head.
As to the comment about the backing up of trains, I have every confidence that this wont happen on mass scale. Train movments will be diagramed so that there aern't any conflicting paths, and there is a staggered gap between trains, allowing for the route to be set for the next train to approach the section, and the previous to clear.