Depending on if you need Bluetooth or not, here are a few real nice HU's:
http://www.millionbuy.com/eclcd5000.html
http://www.millionbuy.com/piodehp980bt.html
http://www.millionbuy.com/piodehp880prs.html
http://www.millionbuy.com/kenkdcx990.html
3-way component simply means three speakers per front door; a midbass, midrange, and tweeter. Instead of the typical 2-way system that usually has a 6.5" speaker doing double duty as a midbass and midrange driver, and the tweeter taking care of the highs.
Find out if you're local stereo shops do fiberglass work, and definitely see if they have example pics from previous customers or a demo vehicle. If they don't I wouldn't recommend you do this yourself since your a car audio newb (no offense).
Which, in that case, we'll stick with a regular two-way system. I can't really start to recommend any speakers unless you tell me what speaker's you've heard and liked. So hit up the local shops, listen to some speakers and note whether they have a silk dome tweeter or a metal dome tweeter. Metal dome tweeters are more vibrant and very clear, but some people prefer silk domes because they find metal-dome tweets harsh.
Yea, something like two 10's will work. If all you need is a little bump to keep up with the front speakers you probably only need one nice 10 or 12" sub.
What kind of trunk setup are you looking to do? Just a regular box tucked in the back with the amps screwed into it, or something more custom with a false floor with the amps showing thru plexiglass?
Since we're not going for a all-out SPL hearing you from three blocks away type of deal don't worry about the batt/alt. The stock units will do fine.
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