One would have thought that Ford would have either offered a complete crate 5.0 drop in engine, complete with everything required.
OR offered a HD version of a 4.6L..... that would just drop in.
Ford Performance currently offers a 460hp Gen 3 Coyote long block crate engine as the "base option" in its line up. You can also buy the Ford Performance Control Pack separately, making it possible to have a running & driving Gen 3 Coyote in almost any Ford vehicle of almost any age.
The problem in some states is getting it to pass vehicle inspections. An ECU from an 11-14 GT that's been reprogrammed with the correct VIN and with the PATS disabled for a swap into an 05-09 Mustang gets around that problem, and Matt's plug n play harnesses take away the headaches from making all the electrics (especially the AC, cruise control, traction control, gauges) work as they should. You could even run the EPAS from an 11-14 GT/Boss if you swap in the EPAS rack and delete the 05-09 PS pump & lines, decluttering the front of the engine.
The only disadvantage of running the 11-14 GT ECU is that you can't pair it with a complete Gen 2 or Gen 3 long block engine. If you're going to run anything but a complete Gen 1 Coyote you have the following "Frankenstein" options:
1. Gen 2 or Gen 3 short block.
2. Gen 1 or Gen 2 (better) cylinder heads.
3. Gen 1 camshafts/timing components.
4. Any Coyote intake manifold but with IMRCs disabled.
You could therefore run what's called a 2-1-1, 2-2-1, 3-1-1, or 3-2-1 Coyote set up.
Alternatively if you'd rather avoid the downtime and complexity of a Coyote swap, you could buy an all-forged 3V stroker short block or long block engine from a reputable dealer e.g. Brenspeed, JDM Engineering, MMR. You'd then have the option of boosting it way past what's safe (~550rwhp & ~450rwtq) for a stock 4.6 3V short block.