As another person who has spent time in the auto industry, I can't speak to Ford as my experience was in Chevrolet/GM, but in our "owner assistance/warranty booklets" there is a very clear disclaimer that the sales guys are supposed to go over which states that any aftermarket product WILL void the warranty. The disclaimer has been there since at LEAST 2004. A good rule of thumb is that modifications to the appearance of the vehicle are ok but as soon as you start to change the way that vehicle performs you will run into trouble.
If it is an aftermarket product causing the issue then going directly to Ford will probably not yield you any results as they simply will not cover a part that they didn't install or manufacture. The way warranty works is the dealer does the work and then the parent company reimburses the dealer. Contrary to popular belief Ford/GM/Honda/etc. do not own their own dealerships, each store is privately owned, so having the work done at a Ford dealership does not mean that Ford endorses or covers the modifications.
As a side note, what did they tell you about returning the truck at the end of lease? GM's policy is the truck must be returned "factory", if you bring them back a lifted truck they will bill you for the labour to put it back to factory condition.
I hate to say it but I think as far as warranty goes you're SOL. If the dealership installed the aftermarket parts then they should cover whatever damage those parts caused.
You're best bet is to stay calm cool and reasonable. Get the sales manager, service manager, and dealer principle/General Manager involved. Point out that you've spent a lot of money both in their sales department and service department and that you would like to continue spending money but you need this issue resolved. As a last resort you could contact
www.amvic.org and they will do an investigation.
Good luck