Doing a Terminator swap into a fox is a big wiring project, as you have to rewire pretty much the whole car, from what I've been told. With a coyote you can buy the Ford racing harness and computer and be done with it.
You can find complete 03/04 Cobra conversions on eBay with engine, tranny, wiring, fuel tank, front accessories, etc for around $8,000-$10,000. Designed around the fox platform. Already supercharged and responds great to bolt-ons. K-member, headers, hydroboost conversion will probably be a must.
You can find '11-'14 Coyote engines on eBay for around $5,000. Plan on spending another $1500-$1700 for the Ford harness and computer. Again, K-member, headers, hydroboost. If you want to keep power steering and power brakes, aftermarket accessory brackets will be needed. Relocating the sway bar brackets and oil filter relocation kit is also recommended. You don't get the T56 tranny like above, unless you buy it seperately. You will also have to get a bellhousing.
There's pro's and con's to both. I personally would go Coyote just to keep the wiring simple.