Brandon,
Personally, I've not seen or touched a SC motor built by Coy Miller. I've heard many good things about the work that comes out of Coy's shop. I've also heard of many people who purchased Coy Miller engines and experienced problems with blown head gaskets afterwards. These incidents may have absolutely nothing to do with how the engine was built or who did the work. I've also heard that unless you're a big roller, and price is no object, Coy isn't all that interested in your business, but again, that is second hand, so take it for what it's worth.
Tom Morana has been building Ford V6's for many years now. He's done extensive work on the 'Stang version, and the SC version. He's also done impressive things with the newer modular V6's, like the Duratec 2.5L and 3.0L engines. Most importantly, Tom is willing to work with you to get your business. You will have the added bonus of bringing your US money up to Canada, and the exchange rate will benefit you. I know Tom stands behind his work, and have learned of cases where Tom fixes or replaces engines he's built, even when the failure was clearly not the result of anything he did or didn't do.
In all fairness to both of these engine builders, I suggest you pick up the phone and call them. Tell them what you want to do, and what your budget is like. See what they have to say. I'm not sure of Coy's contact info., but Tom can be contacted through the information he gives out on his website. Here's the link:
http://www.moranav6racing.com/
Please tell Tom that I said "hello"!
Best regards,
Sean