RPM changes
 

HVAC off. When moving selector through gears, it often drops to about 500 RPM and then move back up to about 600 except 1st which moves back up to about 550 RPM. Neutral has idle of about 725 RPM.
Torque converter stall speeds seem to be consistant.
Is there some sort of relearning for PCM? It acts like it is hunting.
What could be causing this?

Idle does seem like it has mild skip which was there before changing plugs and installing new Visteon COP's. I changed them out for that reason and that water got in a couple of plug wells thus displaying code. No codes now.

That sounds normal to me, mine does that too. The idle air control valve has a small amount of lag to it. Mine has been like that since new, regardless of coil type or plug. I now have NGK Iridiums and granatelli street fighter coils. A master mechanic I know said the small skip was a lean mis. Our trucks have dual cats each side and were considered LEV's. Low Emissions Vehicles. I just took that sticker off the driver front window when
they got tinted. If the RPM's bounces more than once it could be a leak or failing IAC. Also clean the MAF with MAF cleaner.

Another symptom of concern is when I step on it. It seems to have tremendous lag of response. Like an old 8088 computer (8 bit) would be having to think out a solution before the fuel responds, maybe a 1/4 second later.

Yep, just catch up on maintenance and servicing. Disconnect the battery before doing so. :thumbsup:

It's only got 54,000 miles! And it seems to have started using some oil.

What oil was used on the last oil change? With that low miles and it's age it could be sticky rings. I had that issue on another vehicle before. It sat for 2 years. I check compression and it was very low so I put 2 tablespoons of transmission fluid in each sparkplug hole and let sit for a day. The next day I turned it over with plugs out a couple of times then re-installed plugs. It smoked a bit till the tranny fluid burned off but solved the oil consumption. The tranny fluid desolved the carbon build up on the rings. I'm sure jbrew may have some additional Idea's. He is very well known for his knowledge and advice.

its still almost 14 years old! I'd change the PCV. Run some techron through it. Clean the throttle body and IAC.

Oil change was done at dealer. Your guess is as good as mine as to what they actually have in the barrel.

Age should have nothing to do with PCV. I looked at it and appears good. Spring would only be under tension when engine running so it should not have gone yet. TB & IAC are under consideration but will change fuel filter first. An injector is of consideration.
Since I changed all COP & plugs symptoms are about the same. None of the plugs showed unusual signs toward buildup. I'll double check to see if any show too much toward lean side (old plugs).

If you are seeing oil consumption the PCV would be the first thing I changed.

Use a motorcraft one. I did mine at about 70,000 miles when I saw my oil consumption go up slightly and it fixed the problem. For what it cost it is a no brainer to me.

Cleaning the IAC and throttle body is also cheap. A few cans of TBC and your time.

jethat gave you some good tips there and they cost very little.

To some degree I may be disappointed in 4.6 because my first experience was with those in Town cars, the 32V. They were powerful and really moved that big body and even more surprising averaged 28 MPG for 2600 miles of highway, a rental. My sister has a Grand Marquis with 4.6 and mileage sucks on it. I now suspect it too is only 16V. I know years passed and EPA might have stepped on some of it, not this badly though. Were the DOHC 32V unreliable?

I had no idea Ford had gutted that engine to 16V and stuck it in trucks.
That said, I feel you might be right about IAC and throttle body cleaning. I would have ordered PCV as well as fuel filter, etc. but they had no FMC one. I had read somewhere in forum it was important to go back with a Motorcraft.
I say IAC because it is a little rough at idle but running above that seems smooth. Although the programming of the computer seems to suck as downshifts seem too soon and often upshifts are delayed. Like it was programmed only for towing and hauling, never running empty.
I have not seen one or TSB saying one came out, did they make a new program?
(It really needs one)

as long as your back there changing the IAC & PCV....check the Elbow on the Vacuum line that runs to the PCV...make sure it isn't giving a slight leak