Some random thoughts...
Alpine is not as high-end as it used to be, so it may not be the best choice for SQ. If you are looking at it for it's features and ability to "look stock", it is a good compromise. If you want the best SQ, take a look at the some of the Eclipse head units.
You can do a lot better than JL for raw drivers, but if you are looking at a JL box made to fit in the Civic, it will be an OK compromise.
Bring a CD (not MP3) with you that is something that you know sounds better on your home system than on the stock Civic system and that you can easily identify the differences. Jazz tends to work good for this.
Don't base your speaker judgments on the display board. It is not a good comparison to what it sounds like in the car. Ask them to hear their car. If they are recommending something different than is in their car, ask if any of the other people at the shop has them so you can hear what they sound like with your CD in a car.
Focal is a very good choice in it's price range.