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It's directly under the drivers side door on the inside of the frame rail--takes a 6mm allen wrench--be very careful not to strip the hex or you'll be at the dealer getting the warranty work done
Partsman gave you the correct location. When you open the drain, you don't need to drain it for more than about 30 seconds at the most. I believe it holds about 100cc's of water.
You should have received a 6.0L Powerstroke booklet with your purchase. It has a diagram and explanation on draining the fuel-water separator, as well as how to change the filter on the left end of the device.
FYI - I'm going in for warranty work tomorrow for the plug stripping. Not totally yet but close enough. The dealer said they have a fix that replaces a lower part of the housing w/plug. Should take a couple of hours. Don't know how they can replace only part of the housing but...
And if you haven't already, get a 36mm socket for the fuel and oil filter caps. Can easily over/under tighten with a band wrench, etc.
And watch the torque on the 36 mm oil filter nut too. Don't know why they decided to use such a big nut as folks might be tempted to over torque it based on it being such a large sized socket.
A 19 mm nut would have been just fine for that torque.
Don't know how they can replace only part of the housing but...
The water separation manifold (in whose cover plate the drain plug is located) is a little section bolted onto the side of the main HFCM housing. So it's actually kind of handy when the hex hole strips to just replace that unit. And for early trucks, they're likely to *want* to do that anyway, since there was a TSB out about the water in fuel sensor (inside that manifold) getting crudded up and sticking "on" on early trucks.