Uhhhhh.... Why are you keeping the awful stock head unit and trying to 'clean up' the signal by adding processing? Once the Ford unit cuts the amplitude of your low notes, 'reconstruction' is estimating at best, your low end will lack detail, or will be flat when the original recording was not. One should only use this signal processing when they have to, and as you're buying 5 channels of amplification (meaning you're re-running speaker wire anyway) and good equipment, you're doing yourself a huge dis-service by not replacing the brains of the operation. You're buying a W3 (same sub I've got in my Mustang) for sonic detail and accuracy, but your circuitry is taking that away.
A new head unit will have built in, adjustable crossovers ($ comes into play when we talk about how accurate / picky these will be) and will really let that system shine. Also, with this much power, $60 or so for a 1 Farad capacitor will keep your lights from flashing and reduce drain on your alternator during sudden surges of current to your sub. On a personal note, I found that getting two separate amplifiers (400w monoblock into 2 ohm and a 400w x 4) was the more economical route, but this was about 4 years ago. 400w is just right for that 12w3v3, at least in my slightly-smaller SN95