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I was planning a 4.7L swap with Stage 2 tranny from AIR RAM, I was gonna go with an 06 4.7L with the 08 Intake manifold, 70mm TB, H.O cams from ait ram, JBA Headers, Custom 3'' single exhaust with 2.5'' y-pipe, forged piston, forges rods, ARP bolts, Limited slip diff, Gear (unsure), and either 150 shot of nitrous or 16-20PSI of boost from Paxton Supercharger or a Custom STS turbo kits
3.92 gears is what is recommended for supercharged trucks. There is a pretty good debate as to which is better. Some say 3.55s are better but the 4.10s worked great for me.