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
I can appreciate your opinion, as I shared it with systems that I installed in some of my older cars, but the head unit in the shaker systems is actually a very good unit. Will you get better and cleaner with something aftermarket, you can with the right unit. But let's not forget that some of these systems like mine have sync, navi, bluethooth, ipod integration and steering wheel controls. I like the functionality of these features, and don't see the need to re-install them aftermarket. I did that in my '06 F-350, but it had a standard BS ford stereo. With regards to your comment on the signal processing, units like the LC6i, take signal from your factory subs, front, and rear channels. It is not "reconstructing" anything, it is summing the signals together in order to create a full range output. In my system i use individual LOC's, one for the sub signal and one for the fronts. Quite frankly it is the one of the best sounding system i have installed. Plus it looks and acts completely like a stock system, unless you open the trunk, that doesn't look very stock.
As far as a cap goes, I have one in my '85 T/A with a small 5 channel amp and 10" sub, it definitely needs it. But in the 5.0, i am running a 400x4 and a 1000x1 (to 2 12" jl audio subs). I have no cap, no noise, and zero dimming headlights even when i pump that hip hop sh!t.
Now I am just here offering an opinion as someone who used to feel like you, who gave this new approach a try, and was very pleasantly suprised. Keyser Soze is a legend and has my respect so please don't kill me and the family for my opinion. (Usual Suspect was an awesome movie)
2012 GT CS Ingot Silver Vert, Edelbrock E-force supercharger with CAI and 3.5 Pulley, Tremec T-56 Mag, Accufab 84.5, Centerforce DF, Billet Yoke aluminum driveshaft, FRPP 3.73 Rear, MRT Performance H-pipe, Bassani axle backs, JL Audio sound, Edelbrock strut tower brace, JPC adjustable UCA, UMI adjustable panhard bar, KW V3 coilovers, Steeda heavy duty front mounts, Steeda rear LCA's, 20" Steeda Spyders with Michelin Pilot Super Sports, Steeda Big Brake Kit ....... it just keeps going.