Try this, didn't need to do much to line them up.
Switched a couple of connections and unplugged a couple too(the water shader and warp shader don't need any input nodes). Put a negative offset in 'water surface layer' to line the water up to the terrain, I used half the depth of the river's cut for that. Also added a colour adjust to the warped shape to feed the opacity channel with a solid edged river that will extend just beyond the banks.
You probably don't want the water to be displaced by the actual cut either so it's now just displaced by the terrain before the cut and is a bit more flat(ish, the terrain is a bit rough).
Lastly, I put the red guide layer after the 'ground' shader too(and unchecked the blending shader in the 'ground node), that way you'll have the entire ground covered by rock and you can use the following red layer as a base to build the riverbed on top of.
Each time you reseed your terrain or warp shader the river should fit automatically to the new shape.
Hope I haven't confused things too much, I've a tendency to do that.