Hmmm...first I think the exhaust is getting a bit too big actually. With too large of an exhaust you'll lose hp and torque. That's an inline 6 not a 351W or a 460. 3 inch is by far too big and the 2.5" is pushing it. How big is it comin' off of the headers to the cat(s) on the Y-pipe? One or two cats? I'm assuming two cats on the Y-pipe coming off of the headers.
The gears will help. But you'll lose gas mileage if that's a concern. The 4.10s will definitely help out. Also make sure you pull with the O/D off. Do not pull with it on or you'll tear that tranny up. Too much strain on it when it wants to shift into O/D. Especially on hills or grades.
Is your truck two wheel drive or 4x4? Just wondering why you're running a 31x10.5 tire size. If two wheel drive I would back off a little on the tire size. Those larger tires will slow you down and decrease your truck's pulling ability. Even on the 4x4 it'll make a difference but I never cared on my 4x4 cause I needed them for 4 wheelin'.
The K&N will help it breathe better but I don't know how much of a difference it'll make on the 6 cyl.
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1994 Red SVT Lightning #2019