You have two warranties. The first two years are the HD manufacturer's warranty. It is controlled by both CA and Federal laws both of which provide that after market parts and modifications absolutely do not void your warranty. Only if the manufacturer can show your modification caused the failure can it dishonor it's warranty and then only for that particular failure. This is not to say that HD won't claim so.
This is a common misconception.
Harley's warranty covers a stock bike, period. Harley is under no obligation to warranty another manufacturer's parts. Harley is also under no obligation to warranty parts that have failed when aftermarket performance parts are used. If you install something on your bike that is sold with the "for off-road use only" or a similar disclaimer, you're kissing your factory warranty goodbye.
Dealers may work with you and cover stuff, but they're under no obligation to do so.
The Magnuson-Moss Act, despite internet claims to the contrary, does not compel a dealer or manufacturer to fix your bike after you've added a ton of performance stuff to it. What it says is that a dealer or manufacturer can't force you to use their maintenance products in order to maintain a warranty unless they're provided to you free of charge.