When I bought my 06 Mustang I asked the salesman directly if I did a computer upgrade, or suspension upgrade[ford or not] he told me straight
out that the warranty would be VOID. But, htat was my dealership not all. Some may be more lenient?? Unfortunately, i have had experience with AFTERMARKET extended warranties and my advice is to stay the h_ll away from them. If you want the extended warranty buy one from Ford. The extended warranty I bought for my Honda[commuter car] was an aftermarket warranty, however when it came time to use it they were out of business and based out of Jamaica. My mistake, please don't make the same one.
Also, a salesman tells you the factory warranty will cover anything, look for a new salesman, he's lying to get your money. Talk to the service manager to verify what they will cover.[and get it in writing if he says they cover everything.]