Help Please, Getting a Mustang 4.0 to run

I have a 2007 Mustang 4.0 V6 in a 31 Ford pickup. I have the engine and trans wiring harness, the gas pedal, the underhood fuse and relay box and the PCM. I have read articles on EFI and know what the sensors do. I bought a schematic of the car, but have a difficult time following it. It is probably simple to you all, but I can't figure out where to start. The PCM has 3 plugs. I have 2 of them. The fuse box has 3 plugs. I have one plug. Where do I wire in the switch, the ALDL, and the "check engine" light? I also bought a program to turnoff the "PATS", emissions, and a SCT handheld tuner. Of course I need the ALDL to use it. I read an article here about removing all the sensors, lay them out plugged in and remove any wires not connected. I planned to do that after I have it running so I wouldn't remove a wire I needed. Guys, any help on getting me headed in the right direction in getting my engine to run will be greatly appreciated. Thanks

On a 2007,it will not be labeled ALDL (assembly line diagnostics link).
In 1996 with OBDII it is now called the DLC (diagnostic link connector).
The check engine light will be labeled CEL likely,find it in the cluster wiring diagrams.
Pretty sure it communicates over the network,so might need that module wired in and extend the light from the cluster itself -see below cause might need to do that anyway-
That should help you find it with the diagrams.

what program do you have to delete PATS?
As a Ford tech I had a customer with this same project that asked for my help.
His was a ranger 4.0 into a 40's studebaker truck though.
I did alot of reading and talking with other guys and my understanding was even tuning it out doesn't work.

We ended up taking the board/module from the instrument cluster (where PATS module resides) and wiring it in as well as the transciever from the ignition cylinder,sticking a key in it,programmed key to PATS and mounted under dash permanently.

Unfortunately there is no easy way to delete PATS that I know of.
Even at the dealer our IDS computer takes 10 minutes to get into security programming,and no option for turning it off-only for learning new keys.
Unlike GM,there is an actual pellet in the key which transmits a signal to the transciever in the ign cyl.
So no resistor mod etc.. will work.

Thanks very much for the help Playtoy_18. I appreciate the help. The program to turnoff the PATS is from SCT. They said to plug it in when I get a signal from the engine. After the program is installed I should be able to run the engine.
I finally gave up trying to do this myself. I took my mocked up chassis to a local Mustang tuning shop. I showed them what I have and they told me that they can fix it so it will run and the trans to shift properly. They said that they recently finished doing a 4.6 3 valve in a 32 coupe. I guess I'm an old dog and not learning new tricks. I'll let you all know how it turns out when I get it back.

I've not dealt with PATS disable past the '04 architecture, on paper you should be able to disable it through the ECU. If for some reason you can not, contact me. I have some n,on-SCT access to those ECUs, and the ability to disable PATS (although I've never tried it).

Also, thats a super cool project. You should post pictures!

Thanks mekkis, The shop that told me they could get it running now says they don't have time and I need the gauge cluster and all the harness before they can even start. One tech did suggest using an older PCM totally. I am going to the junk yard Monday to see what I can find. My engine was used in Rangers and explorers since the 80's. Any suggest on what year would be the best? I think I would like to stay in OBDII era. I tried to post some pics, no luck. I'll try again. Thanks for the offer, I keep that in my head.