Ok, lets see if anyone can figure this out.
1999 F150 XLT 4x4 Off Road extended cab 139" W.B., 5.4 L, A/T no mods to anything
I had a reputable mechanic look at the truck when I ran my HVAC business because it had poor performance and would fall on its face at highway speeds randomly. His mechanic said it had low compression on #3 cylinder and would cost $1100 to open it up and find problem, I didn't believe this but didn't want to spend that money and then get taken for more. I pulled it in my shop and tore the top end down took heads to machine shop and while they were away I dropped #3 to bottom of cylinder filled with trans fluid and monitored for two days, guess what no leak-down, repeated this on all cylinders until getting heads back machine shop said there was no problems. I reassembled and it ran ok but had a whine. The truck would still fall on its face randomly, so I took to the local Ford dealer and let them investigate, they said they cleaned the injectors because they had some residue at nozzle. Ran ok for a while so once again I pulled it in my shop and this time removed the injectors and found the same residue in injector nozzle, I used a piece of 22 ga. wire to dig the residue out and tested by smelling, looking at under magnification, and feeling. The substance was sugar, I replaced the tank, pump, filter, injectors and flushed the lines with both brake line cleaner and finally carb. cleaner put all back together and problem of falling on its face was solved.
Now to the whine, I first began eliminating possibilities of the engine by removing the serpentine belt and isolating the engine from the driven accessories and found no while. next I listened to Alternator and could hear a slight bearing noise so that was changed, but whine still there. next was idler pulley replacement and no difference, next was the tensioner replacement with no replacement and no difference. I let it go for a few months and noticed the noise changed when the A/C was on, so being a HVAC tech. the compressor was changed with no difference. The only things remaining were the P/S pump and water pump, I changed both of those and the damn noise is still there, any suggestions would be appreciated.

 

Well it sounds like you had no whine until you reassembled the engine. Since you have changed all the FEAD components I would suspect the timing chain or HDR wheel. If the crankshaft timing gears are on backwards they will generate a whine same goes for the HDR wheel being on backwards these two parts will make contact with either the timing chain or the timing chains are making contact with each other and or the front cover. If a chain is out of the slot on the chain guide it can make a noise as well. Also check that the chain tensioners do not have a 8mm pipe plug in either of their oil supply holes that are in the cyl head right behind the tensioners.I have seen cyl heads after mechanics have worked on them with 8mm plugs installed behind the tensioners. Some guys see these holes and think a plug is suppose to be in them, you then have no oil going to the tensioners and the chain will run dry on the guides making a whining noise.

 

Might be a dumb question, but I have to ask. Did you put the wrong fluid in the power steering? I've seen people do this all the time, and it causes a whine, and eventually seals fail. Your truck requires Mercon or Mercon V to be used. Nothing else. No additives, no conditioners, none of that Lucas sh*t, just Mercon. If improper fluid was used, flush it out and install an in-line power steering filter to prevent further damage. Probably won't do much to fix the noise at that point.

You really should invest in a mechanic's stethoscope if you don't already have one. They're cheap, but irreplaceable for tracking down things like this. You may hear the whining all over the place with it, but when you find the source, you'll know it.

 

DYNOTECH, I checked for noise from internals by removing the serpentine therefore only the engine components such as timing chains, gears, tensioners and guides, or valve train components and even the rotating assembly would be able to make the noise. When this procedure was performed there was no noise, but I will remove the serpentine belt again and re-check.

 

EsJayEs, I don't believe there are dumb questions otherwise how do we learn. To answer your question, yes I did use the correct fluid, and no I don't have a true stethoscope but use a long screwdriver to listen, however the noise was present prior to removal of the factory pump which had the same fluid prior to the top end of the engine tear-down. I don't remember without re-reading my terribly long original posting but I changed the water pump this January because it was starting to make a bearing growl, and this didn't change the noise either.
By process of elimination the only thing that hasn't been changed is the fan clutch, so checking that is probably going to require the stethoscope since I can't put the screwdriver on the fan shaft.

 

Did you install a new belt when the engine was reassembled? If so what brand?

-Steve

 

Fan clutch is really easy to eliminate. Take the fan off and see if the noise goes away. Do it with the engine cold and you can run it for ten minutes or so without getting too hot.