The warranty is thru carmax not ford. It does still have the factory warranty but I think its 3yr 36k the carmax warranty is 5yr 150k miles.
I'd be more interested in a tune then anything else and I know a tune is the one that is the grey area. I'd be nice if someone local had some mods that I could hear before.
I'm a bit paranoid about the warranty and tuning issue as well, so I had done a ton of research before I even bought the kit. Here's what I found... what it comes down to:
By law,
whatever company is covering the vehicle warranty (whether OEM or 3rd party contract) has the burden of proof to demonstrate that the damage is not the result of a defect, but the result of usage not covered by their warranty product.
The warranter's contractual obligation extends only to the service they agreed to provide for the item(s) they agreed to provide them for, in accordance with the contract. For example, if you install an aftermarket muffler, it's not covered since it wasn't on the car when they warranteed it. However, putting on the aftermarket muffler won't prevent you from getting your broken door locks fixed, which would still be covered. This much goes without saying. Likewise, getting into a wreck wouldn't invoke their obligation either, since the damage was the result of usage that isn't covered. (In this case, your insurance would foot the bill.)
If you installed that aftermarket muffler, and have an engine failure after you did so, they might (possibly, if they're really sleazy) try to claim that the muffler somehow caused the failure due to difference in backpressure, blah blah blah. After all, businesses will
always do whatever they can to increase their profits.. that's their reason for being. On the other hand, you of course will claim the engine was defective, and not destroyed by the muffler. Now, in this kind of disagreement, the law needs to decide. The law is there to protect both parties. It protects the warranter from abuses by the customer, which might try to claim that something they broke through misuse was simply defective. It also protects the customer from abuses by the warranteeing company, so they can't claim that your choice of car soap weakened the gloss on your ride, subsequently increasing drag on your car and therefore stressing the suspension, therefore increasing the jiggliness of the vehicle, resulting in engine parts getting scrambled about, thus resulting in engine failure... because you chose X brand soap.

(With that kind of silly logic, no warranty would be honored...
ever!!)
In all seriousness, the laws on the books exist, and if the warranter wants to claim that a part resulted in the failure of another then, they have the burden of proof to demonstrate that it's at
least possible
and likely. (I doubt they're be required outside of court to provide concrete proof per se, but I'm not a lawyer... I suspect that they only need to prove that it's
reasonably the cause of the failure.)
In the case of tuning, I would say that an overly aggressive tune
could cause damage, but I don't think any
responsible company would even sell you such a tune. If the warranter states they believe that your tune was at fault, and if you can provide documentation that demonstrates your tune was very mild (from the perspective of material/product tolerances, not how fast it makes you go), and that X out of Y number of vehicles have the same tune
without a failure, then
they would then need to prove conclusively that it
was responsible.
There is a huge downside here though... if it came down to it, and it needed to go to court, while you could probably win, it would cost you far more to defend your position than to buy a new vehicle. And I'd be willing to bet that Ford, or even Mom & Pop Warranty Co., would bank on you not wanting to accept such a financial loss to
just prove you're right, and can therefore claim whatever
they want. (Now if there were a TSB related issue, I think that might change the picture quite a bit, because not honoring a warranty on a known problem could create a loss for them if it gets out that they're not honoring their own TSBs, and therefore lose sales, regardless of the facts of the case... that's just my take on it though.)
So what it ultimately comes down to,
in my own opinion, is this: Accept the fact that whatever you do to your car
won't void the warranties, but if there's
any chance that your vehicle will need potentially related parts or service under warranty (transmission, engine, etc.), and you're not willing to pay for those particular repairs out of pocket, then you need to factor that into your decision to modify or not. Assume the worst, hope for the best.
As for me, I simply don't plan on drawing attention to my tune, and if any of my parts are indeed defective, then I'll just hope for the best until I hit that 60,000 mile marker. With any luck, I don't have any defective parts, and even if I do, I hope that no one will notice that it's been tuned while those parts are getting looked at.
That's my two cents.
Sorry for the super long post. lol