LaserRed---Brace yourself, this is gonna be long. I had the exact same question posted in the Female Forum, and got this link from Dark Knight. He is forevermore my hero!
http://www.alternativeauto.com/water.../warranty.html
Go there and print out the info and keep it with your warranty papers. It applies to any modification.
Now then, I also quote directly from my onwer's manual (probably identical to yours) on page 22: "NOTE: FEDERAL WARRANTY ONLY The maintenance, replacement, or repair of emissions control devices or systems, the cost of which is not covered by the warranties, can be performed by any automotive repair establishment or individual using non-Ford parts."
"For vehicles within the warranty period, Ford will repair at no cost to the owner, under Federal Emissions warranty, covered emission failures caused by properly installed Ford parts or non-Ford parts that have been 'certified' by the US EPA. Ford is not responsible for the cost of repairing any emission failures caused by non-Ford parts that have not been 'certified' by the EPA."
In a nutshell, the EPA mandates that Ford cannot "ding" us for warranty work on the emissions system, whether Ford or aftermarket parts are used, as long as the system/parts are "certified" by the EPA and properly installed. This is a Federal Warranty that overrides Ford's warranty, and applies only to the emissions system.
As for the rest of the car (non-emissions stuff), we have many laws on our side. However, that does not mean we are "out of the woods" because, just as in any other legal battle, we may have to go through h3ll even though we are right. If the car is laid up needing warranty work, we may spend ungodly amounts of time/money/aggravation getting Ford to comply. Meanwhile, the car either goes unrepaired, or we spend unnecessary money (which we recoup later).
So, just know in your own mind that you can mod the car, but be prepared to possibly do battle at some point in the future. Just because we're "right" doesn't mean it'll be easy. Make your decisions based on that knowledge.
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"Back in the day"-Red '66 289
"Later"- Black '68 289
"Today"- White 2000 GT
Stock except K&N & Flowmasters
ET-13.952@98.87 RT-.507 60'-2.09
Son #1 - '87 GT stock
Son #2 - '89 LX 5.0 stock