Ok...I've searched this forum from top to bottom and side to side...no one seems to have the same issues...
My truck- '99 F150 with 4.2v6, 4R70W auto trans, manual transfer case, and open rear diffhas been acting up for the past few months. It started with what seemed to be a misfire/stumble off the line and when cruising under light throttle. No check engine light...Changed plugs to Bosch plats....bad idea...got worse. Looked into it here, went back to Motorcraft double plats. Problem still there, no better. Changed plug wires...Motorcraft OE....no difference....At this point I gave in and removed the oversized tires and brought it in to the dealer to be fixed under warranty. Dealer made me pay 90 bucks for diagnostics so they could tell me that they couldn't find the problem cause the computer wasn't telling them what was wrong...they did hook it to a scope and found a misfire that would move from cylinder to cylinder. I couldn't get them to try swapping out the coil pack to see if it would cure the problem. They basically said come back if it gets worse or if you get a check engine light. They suggested getting the tranny fluid flushed. Needless to say, I wasn't very happy and vowed not to give them any more money. I got the tranny fluid flushed...no change. Took the ohm meter to the coil pack, resistance across the coils read a little low... I got excited and thought I had the problem by the throat, until I changed the coil and nothing changed, although she idles a little smoother now...That problem is getting worse, and a new problem has come up that I suspect is the rear end...Seemed to be classic u-joint problem...I replaced the u-joints and the problem is still there. From dead or rolling stop, there is a grinding type noise/feeling from the rear end area, most of the time accompanied by a few clunks that I would associate with slipping gears. I've said enough is enough to my previous method of replacing parts until the problem goes away and need to figure out what the problem is....Any ideas????? Very sorry for the length of the post...didn't want to leave anything out.

 

Have you checked carefully for vacuum leaks? Cleaned your MAF sensor? Try plugging the hose to the EGR valve and see if that makes any difference too.
How does the oil look in the rear diff? Any big chunks of metal on the magnet on the plug? Does the noise go away at higher speeds? Does it change when you're on or off the throttle or brakes?

 

Haven't checked for vacuum leaks....the best way is throttle body cleaner, right? I've cleaned the MAF. i'll check the EGR...thought that would throw a code, though...I've changed the fluid in both the front and rear diffs...Didn't want to spend a small fortune for synthetic so I just went with 85w90...that should be ok, right?Nothing but a pasty buildup on the magnets on the plugs. The noise from the rear goes away before you ever get out of first gear. Once in a while it will clunk when you're on the throttle pretty good and go over a bump. At take off it clunks usually if there is some gravel at an intersection or something, when it spins a little and then catches. Of course it does it worse if you give her more throttle. But unless you take it really slow from take off, there is that grinding feeling/sound... I'll investigate some more on lunch break tomorrow and get back with my findings...

 

Well, can't seem to find any vacuum leaks...plugged the EGR hose...no difference...applied vacuum to egr valve, and the engine started to stumble...that means all is good with the egr, right?

 

Yes that means the EGR is probably ok.
What did you use to check for vacuum leaks? I usually use carb cleaner spray.
Did you try cleaning the MAF?

 

Yup, MAF is nice and clean as of about a week ago...I used the same throttle body cleaner to check for leaks as I used to clean the MAF....I thought I heard somewhere that carb cleaner can be bad on fuel injected engines...something about plastics or electronics or something?

 

I always use Carb Medic carb cleaner spray and havent noticed or heard of any problems because of it.
I wonder if you can find a buddy with the same engine that you could swap coil packs with to try it. It only takes a few minutes to swap them.

 

I replaced the coil pack a day or two after I cleaned the MAF....a near useless venture...90 bucks and it didn't solve a thing, although the old pack tested bad.

 

I'm starting to wonder if maybe the torque converter/tranny/trans case might be the source of both problems? That's what a misfire sounds like....torque converter clutch slippage...maybe the clunking is being transferred through the hollow driveshaft to make it sound like it's the rear end? I dunno...I'm out of ideas...maybe I'll just drive it until it breaks...easier to find the problem that way...

 

How many miles are on the patient?

Do you have a chip? A chip with a loose connection can cause a misfire across all the coil packs.

 

61.000 miles....no chip yet....got to get her running right by her own brain first...