Terry, all of the information that I have shows the exact same block, crank, rods, and pistons going in the 1999 Taurus, Lincoln LS, and Jag S Type.
You are correct about the water outlets. The block has two same diameter core plug holes at the top of the block. LS and Jag plug the rear one and put the water outlet in the middle one. The Taurus just reverses this. Same plug is used in either hole but different water outlets.
Thus, no machining differences. Can you give an example?