New ecu, now no start. No crank.
 

I had a P0351.

Replaced the ignition coil. That did not fix it.
Replaced the plugs. That did not fix it.
Replaced the wires. That did not fix it.

I got an ecm from a local yard. With that ecm in, the van won't crank at all. I hear something clicking under the dash, but nothing.

I can connect to the ecm through the obd port but that's it.

Do I need to do something special when changing the ecm? First thing that comes to mind is some sort of anti-theft thingy that would link my key to the ecm...

2006 Freestar SEL 4.2L

You are correct suspecting the PAT system.
Be careful, and stick with your original PCM.
Any other PCM has to have the key codes from your original keys programmed into it.
If you must replace the PCM you will either have to have a locksmith with the right equipment or the dealer reprogram it. If someone has a Ford IDS tool they can do it, but not very many shops have it.
Where did you have that code read? Not sure if it applies to your vehicle.
What type of problem are we trying to correct?

I have my own code reader so I read the code myslef.

It started a few week ago by running rough, and it got worst over time. It'd skip a beat, then 2 beats, and now it's like watching porn on a dial-up connection. It does it also on idle with no load applied, so still on Park.

The ignition coil had cracked on top where #1 is, and there was another crack in the bottom where the glue or filler is. It looks as if a capacitor exploded inside, or something expanded enough to crack open the casing.

Spark plugs on the rear bank were darker than the plugs in the front bank and were the original plugs to boot, and the wires was a "I hope it's just that!" type solution.

I think it's possible that what ever happened in the ignition coil, made its way back to the ecu and fried something. Besides, what's more to check? I'm open to suggestions.

Regardless, I'll call some dealerships around here and see what they can do for me as far as reprogramming the ecu.

From what you describe It could be the PCM, but it's important to chase down why the plugs on one bank are running rich. The PCM doesn't usually do that.
The PAT system doesn't usually affect running quality, it will interfere with starting .
I hope you did not create addl problems now with the other PCM installed even if only temporarily.
If you can, do a very thorough check of all wiring connections and plugs (not spark plugs).
Poor connections can drive a tech nuts.
The plugs on the one bank could have been affected by the defective coil.

I finally got a chance to bring the van to the dealer to reprogram my keys and it appears the new ecu fixed my initial problem.