wait to start and water in fuel light flashes and truck wont start

[tubbykid]

first off hello to everyone as you can see im new to the forum......the last two days i have read probably 100 different post on here and known with the problem im having......lol.....ok i have a 2000 ford powerstroke and here in the last two days it has gave me some fits........when it quits running the wait to start light and water in fuel light comes on and flashes also the battery light blinks but my gauge reads that the volts are fine. now then along with the lights flashing there is a clicking noise that comes from under the dash and also from the relay box under the hood......if i leave the truck sit for awhile some times 15 min or as long as 2 or 3 hours it will start back up......i have tested the batteries and they are fine and i replaced the crank sensor about 40000 miles ago also fuel filter about 500 miles ago.......well if any of you have any ideas it would be great to hear them cause i am confused.....lol.......thank you in advance

[greenbeast]

You may have a problem with the fuel bowl heater shorting out but not blowing the fuse. Try un-plugging it off your fuel bowl and see what happens.

[tubbykid]

i unplugged the fuel bowl yesterday and tried starting and again it wouldnt start........im getting ready to put a cps on it but im not sure that is it either.....the way these lights flash is throughing me off

[greenbeast]

Do you have a chip in it? If you do it may have connection issue.

[tubbykid]

i changed the cps and still wouldnt start......these lights flashing has got to mean some thing

[ToMang07]

I bet one of your batteries is shot... pull them both and have them load tested. Wouldn't hurt to check the alternator, too.

[tubbykid]

i did have the batteries load tested and the alt. and those stupid lights still wouldnt go off.....so the one guy mentioned if i had a chip in it and i remembered i had put a superchip in it 10 years ago so i pulled it out and it started right up and as been running for almost an hour and half.....so hopefully that did it.......thanks for everyones help