If the car can be put back into alignment then that's one issue out of the way. If you can't get it back to spec you'll either have to hog out the c/c plate bolt holes in the strut tower to allow the stock plate some freedom or you'll need aftermarket c/c plates.
The other issue will be bump steer. Lowering that much increases the relative difference in angle between the tie rods and the a-arms. This tends to magnify bump steer. One solution is to use an offset steering rack bushing which helps get the steering rod somewhat parallel to the a-arm, which decreases bump steer a little. Another solution is a bump steer kit that allows the tie rod end to be adjusted.
Some folks don't bother and live with the bump steer. It's not that big an issue if you don't push the car hard regularly.
Dan
2003 Cobra convertible With some stuff and thiings