Recommendation for Headers/Exhaust on 416

So, 3" exhaust, thru mufflers, slows it down?

It's a combo dependent things and your combo is mello by compare to what could be done and what it's being used for isn't a strip monster.

A 3 inch exhaust will increase top end once you get going no doubt, but it could loose some bottome end power. I said COULD and not will.

The best exhaust is free flowing non-restictive movement of exhaust gas.
IF the (Exhaust) gas stays hot, it'll want to escape quicker than cooler (Exhaust) gas.

Cooler exhaust condesnses and slows down. Thus is also the popular addition to headers like the coating or wrapping of the pipes.
Drag cars use a shorter system since tail pipes extend the system and offer more resistance in it's over the axle bends.