How many miles/what is the build date? Power train warranty is 5yr/60k without any additional warranty, that may be an option, not sure on your mods or mileage.
I would say built 3.5 would be a heck of a lot easier to install, and has already had the road paved. I don't think anyone has done a 5.0 swap on these cars, and I'm not sure if it would bolt in or not. After that, figuring out what transmission, suspension changes as well that may be necessary. Computer changes, etc. though Ford does have a controls pack for the coyote.
My .02 is that the stock 3.5L is extremely stout, and the gains I have seen from built 3.5L for the cost may not even be worth it, but that will be a much easier route and what I would recommend.