2004 F-250 extended cab system?

I'm going to install a system in a 2004 F-250 extended cab and am looking for some opinions. I'm going to remove the back seat to make room for it. I was thinking of installing the following: Head Unit/GPS-Pioneer AVIC-Z1; Subwoofers-2 12" JL Audio W7's (I was also looking at Alpine type X's, which are about half as much, any opinions?); Amplifers-2 Crossfire 1000D's and a Crossfire VR404; Interior speakers-I want to put a 6X8 component system in the front, but I don't know what to go with yet, and a set of 6X8's in the back. I currently have an optima yellow top battery and a 140 amp alternator. I was going to add another optima red top, is there anything else I need to do to the electrical system, I figured with that I should be fine? Any opinions or help here would be great; I have about a $4000 budget.

Well that's a helluva budget.  Priority one is to choose the front components, and they won't be size 6 X 8.  Priority two is to choose a worthy head unit.  These should both be considered first priority, I guess.  Look for quality in the deck other than the list of features.  I would put Pioneer decks down toward the bottom of the list, only because of ground plane issues I've heard about.  And read the "Upgrade the Big Three" featured topic.

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Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.

Yup, sideline the Pioneer headunit and sub in the far superior Eclipse AVN6600. Speaker size in this vehicle is 5x7" (or 6x8" if you must), but, one can easily fit a oversize 6.5" speaker in the door when a 1/4" abs mounting template is made. Do not make it out of mdf as there is moisture in the door and the mdf will warp in no time flat. 14" black abs is what you are after. Keep the rear speaker factory size if you like or upgrade them to a good basic oversize 6.5" coax as well.

As far as power goes, you need more in the front and rear to even begin to think about keeping up with the subs. If you can find a old VR804 (yes they made a super large 4 channel amp), go for it. Otherwise, use a VR402 on the front and a VR202 on the rear. (or if the fashion police are after you, a pair of VR402). Nothing wrong with the W7's, they are a great sub.

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Top Secret, I can tell you but then my wife will kill me.

Do they sell a mounting plate to go from 6X8 to 6.5, or does it have to be built? where can i find the abs, if it has to be built. Thanks for the help so far. Any opinions on a good set of 6.5's?

I think metra makes one, the only problem you will have is finding someone who carries it.  Much easier (and cheaper) to get a sheet of ABS plastic most shops will have some you can buy.  I believe that Alpine makes a set of type R 5x7 componet speakers if you don't feel like making a plate.  I think they sell for about 165 at most places

best kits also makes a 6X8 to 6.5 adapter plate part number BKSA68 im using them in my 2007 sport trac and they work great. a set of Alpine Type R is doing the trick for me. the audiophile i am make me partial to the alpine equipment line. i also have them i the back doors at well. www.4electronicsdeals.com has them for $8.30 they are preconstructs and fit perfectly.