Describe the sound a bit more in detail. Does it sound blown, distorted, or no bass at all?
Setups look ok. Try and keep your power wire isolated from RCA and speaker wire to have less noise. Ground looks good and make sure paint is sanded off there on the chassis. Just apply caulking, vaseline, or rust paint around if your worried about it rusting over time.
Not sure on the Sony amp powering 2 12 kickers. Post some links up or more specifics.
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2011 Kona Blue MT82 V6 Mustang Pony Package 3:31 Gear Ratio, Interior Upgrade Pkg, Security & Shaker500/Sync
Mods (in order of installed): AM Bama SCT SF3 Tuner w/ 87 Hybrid Tune, Airaid CAI, Hurst Billet Plus 2 Short Throw Shifter, Lethal O/R H Pipe w/ Stock Exhaust, Blacked-Out Tints on Rear Windows, Full Ceramic Tint on Front Windows, Metra Touchscreen Dash Adaptor, Single DIN Head Unit, 6.5'' Component Speakers Fronts, Stock Rear Speakers, 10'' Sealed Subwoofer, 4ch. and 1ch Amplifier. LED licence plate lights, LED interior dome lights, FRPP/Dynamic shocks and struts, SR Performance lowering springs, GT500 Strut Mounts, BMR Adjustable Panhard Bar, BMR LCA's, BMR Relocation Brackets. Rear Seat Delete.