Of the 2 the Cobra engine is drastically easier. You don't even need the harness. The Navi engine is going to be way more advanced and require some custom stuff done. I would not go that route.
That said, if this is your daily and you've never done a swap before (which I am assuming since you asked the question about the Navi engine)... get a beater or have a mode of transportation setup other than this car because you will run into a few things.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.