Man I would LOOOOOOOOOOOOOOOOVE to see a sticky summarizing what is needed to do a coyote swap on the 05-09 cars, without using the control pack. I want EPAS and the alternator in the correct location. That and an MT-82.
Also, I am loving your progress. It is a genuine inspiration. Congrats!
I used:
A stock Mustang PCM (bought from a junkyard for $250, I think)
2 Bosch O2 sensors (Amazon, $50 ea)
11+ MAF sensor (eBay, $50 new)
Stock intake, but you could use a CAI. I got this in a trade.
Junkard 11+ throttle pedal ($50?)
I bought O2 sensor pigtails, but I would STRONGLY suggest ordering CR3Z-14300-EA harness. It is the battery/manual trans harness and comes with
Front and rear O2 connectors
Trans wiring
Starter wiring
EPAS wiring/pigtails
Alternator pigtails
PCM connector to make it a direct plug and play
If you use that harness, you will need to buy 7U2Z-14S411-KA pigtail, then solder your CAN BUS, alternator comm wires, starter, and EPAS switched power into this. You could just de-pin from the plug that comes on the CR3Z harness, but I opted for a cleaner installation.
If you purchase the CR3Z wiring harness and use a TR3650 until you can afford an MT82, then you will have to pin in the speed sensor to pin 14 IIRC. I also pinned the clutch switch into pin 19, which I believe you will have to do regardless of transmission used.
The throttle pedal will have to be de-pinned from the 3V pedal (uses 6 wires) and re-pinned to the Coyote (uses 4 wires), but you can use whatever color wires you want from the 3V pedal, just make sure they match at the PCM. This stuff runs through the body harness. CAN BUS will also run into the body harness, but you will have to T off from the CAN BUS to feed into EPAS and into the PCM.
If you have specific questions, feel free to ask! I'm sure I'm forgetting some stuff, but it's really fairly simple, just time consuming. The harness I'm telling you to buy is a MASSIVE time saver, and a must if you're doing EPAS. If you want to do the alternator, buy the M-8600-M50BALT kit from Ford racing. It comes with an idler, tensioner, Boss 302 alternator, belt, and alternator. You can use the Power By the Hour AC bracket to use your 3V compressor. You would just have to order the stock 5.0 AC stretchy belt. I bought some downstream O2 sensors so that I could have FAOSC enabled in the future, which is supposed to keep the front O2s properly calibrated.
You can use 3V PCM connectors, but you will have to shave the PCM side plugs to make them fit, but a couple minutes with a razor and everything plugged right in! However, if you buy the harness, you will only need to do that with one connector. I also needed to buy 7U2Z-14S411-KB to supply VCT, injector, and coil power to the engine.