Okay, first. Honda would have to cover it if it was installed by a professional. Unfortunately it sounds like you did it yourself.
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The amp is connected to the battery in the engine area and grounded both to the floor of the trunk and to the HU ground in the dash. The HU is just wired from the factory wires. It's only a 420w amp so it's not big and it's not turned up to full either.
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Second, you said your amp has two grounds. One to the floor and one to the headunit. You should only have one. Generaly an amp has a wire for ground, a wire for power, and a wire for remote turn on. Power comes directly from the battery (like you say it is), the ground goes to a ground point (the floor of the trunk is okay for this), the third wire usualy goes to the power antenna wire or accessory wire that has +12v when they key is on or in the accessory position.
What I would do instead of taking it to the dealer is taking it to a repuatable car audio shop. They can probably repair anything you did wrong or at least get the radio wired correctly. Then I'd take it to the dealer if the car doesn't recover on its own.
I am running much more in my car than you are and I haven't had any problems.