The Warranty Manual spells it out pretty well:
The New Vehicle Limited Warranty does not cover any damage caused by:
• Alterations or modifications of the vehicle, including the body, chassis, electronics or their components, after the vehicle leaves the control of Ford Motor Company
• Tampering with the vehicle, tampering with the emissions systems or with the other parts that affect these systems (for example, but not limited to exhaust and intake systems)
• The installation or use of a non-Ford Motor Company part or software (other than a certified emissions part or software) or any part or software (Ford or non-Ford) designed for off-road use only installed after the vehicle leaves the control of Ford Motor Company, if the installed part fails or causes a Ford part to fail. Examples include, but are not limited to lift kits, oversized tires, roll bars, cellular phones, alarm systems, automatic starting systems and performance-enhancing powertrain components or software and performance “chips”.
So basically any issue/concern that is attributed to the change in suspension angles and ride height is not covered under warranty. That would include things like CV joint/boot wear or damage, control arm bushing damage, ball joint wear, driveline vibrations, etc.
