1. You'll need an 11-14 GT ECU, engine harness, and instrument cluster. The ECU would need to be reprogrammed with the PATS disabled in order to prevent a no start situation, and with your VIN to make it road legal.
2. Forget about getting either a new or used Gen 3 long block. If you use an 11-14 GT ECU, your engine will need Gen 1 camshafts/timing components and either Gen 1 or Gen 2 (better) heads. Gen 3 heads are no good to you because they're designed for both direct and port injection. Therefore the only Gen 3 engine component you'll need is the short block. You'd then be doing what's dubbed either a 3-1-1 or 3-2-1 Coyote swap.
3. You could also bolt LT headers and a Gen 3 intake manifold onto your "Frankenstein" long block before lowering it into the engine bay. Your ECU would then need to be custom tuned but you'd need that anyway.
4. If you're dead set on a full Gen 3 Coyote engine swap anyway and live in a state that doesn't have Gestapo-like emissions inspections, you could opt to use the Ford Performance Control Pack appropriate for your engine and transmission.
Do you have the dyno sheet? What mods did it have?