I'm in the process of doing all of this as well, in fact the alternator issue is my hold up now (need juice and lots of it). Looking into what options I may or may not have. Anyway.

I would certainly stay away from the factory speaker wire. The fader, at least in my car, will lower the impedance seen at the deck (or amp) as you fade (or I should say have front/back both at full tilt). So depending on what speakers you have, if you are running at the lowest safe impedance already and use that fader, you may present too low of a load for your source. In low power applications and not pushing it too hard, not a big deal (and blowing fans on your amp can be a great remedy), but there is the chance of putting your amp into protect mode. And the old speaker wire may get hot anyway, with more power flowing through it. So I would say stay away from that in any way possible if putting in a system.

I also agree with rebuilding the rear deck if you are mounting aftermarket speakers. Baffle resonance can give some nasty sounds, so if you can hang that speaker in something like 3/4" material, you'll be much happier in the long run. Same goes for any speaker you mount. The more dense the material you mount the speaker to, the less chance of resonance from that at least.

Personally I'm not so sure that you will be happy with deck power (13 or so watts) to the front speakers and then have 40 watts per going into 6.5's in the back. The rear will definitely overpower and will pull your sound back considerably. Of course, alot of people do not necessarily care about sound stage either, and just want a more "full" sound in their ride.

The cookbook would be a great idea. It will shed alot of light onto cabinet design. IB applications are not for every sub. You'll definitely want to check the T/S parameters of your driver and make sure that it is suitable for that. IB will give you a more "natural" sound, but the trade off is that power handling and output are cut in half at best. Its easier to bottom your sub out and cause damage to it in IB for those reasons. Also, I wouldn't mount the basket up, if you are looking to reverse the phase of your speaker, simply reverse the +/- at the speaker. That will help with cancellation issues if that is the reason why you want the basket up.