I found these list of steps on another forum. Yikes...
Raise and safely support the vehicle.
Drain the cooling system.
Loosen the exhaust flexible pipe clamp and disconnect the 2 exhaust hangers.
Remove the 4 nuts, the exhaust flexible pipe and the Y-pipe as an assembly. Discard the nuts and the gasket.
Remove the LH and RH catalytic converters. Refer to the Exhaust Manifold procedure for more information on catalytic converter removal.
If equipped, remove the heat shield and disconnect the block heater electrical connector.
Remove the RH cylinder block drain plug or, if equipped, the block heater. Allow the coolant to drain from the cylinder block into a suitable container.
Remove the LH cylinder block drain plug. Allow the coolant to drain from the cylinder block into a suitable container.
Remove the engine front cover.
Rotate the crankshaft clockwise and align the timing marks on the Variable Camshaft Timing (VCT) assemblies
Install the special tool onto the flats of the LH camshafts.
Install the special tool onto the flats of the RH camshafts.
Remove the 3 bolts and the RH VCT housing.
Remove the 3 bolts and the LH VCT housing.
Remove and discard the VCT housing seals.
Remove the 2 bolts and the primary timing chain tensioner.
Remove the primary timing chain tensioner arm.
Remove the 2 bolts and the lower LH primary timing chain guide.
Remove the primary timing chain.
Remove the 2 bolts and the upper LH primary timing chain guide.
Remove the RH primary timing chain guide lower bolt.
Loosen the RH primary timing chain guide upper bolt. Rotate the guide and tighten the bolt.
Remove the 8 bolts and the water pump.
Thoroughly clean and inspect all mating surfaces.
They say it's like a 12 to 24 hour job just to replace a water pump. I am inspecting this picture of the 3.5L and I can't tell which one is the water pump, but it being inside the engine really shows that if it fails and starts leaking, it'll just go into your oil and kill the engine... Ford built to break completely if all goes wrong.
http://www.blogcdn.com/www.autobloggreen.com/media/2008/08/zz7a5ad63a.jpg
EDIT:
http://www.gminsidenews.com/forums/f57/ecoboost-engine-flaw-74380/
This forum tells of wheep holes or drainage holes but I wonder if that's true or not. I'm really concerned about my water pump failing now. Seeing how my friend's 2002 Golf just had a water pump failure, and warped the block with overheating.