Not a tough decision to make, really. On any kind of street car, I like to use what the factory did as a guide. So lets look and see how the factory handled it.
First, even though you're not going auto, lets throw it in for comparisons sake. An auto has a torque converter. It multiplies the torque it sees from the engine, usually on the order of around 2 to 1. I know most probably are like 1.5 or so and not 2 to 1, but for arguments sake, lets say it is 2 to 1.
In the case of the auto, since torque is multiplied, the vehicle can stand a higher (numerically lower) gear. Most factory auto cars used gears in the 2.76-3.23 range. 3.55 was considered a performance gear for an auto and was usually an option.
Lets look at the 4 speed. Here for a coupler from the engine, we have a clutch. It's either engaged or disengaged. There is no torque multiplication. Conversely, there is no slippage at highway speed, either. Remember, unless a converter is a lockup unit, it never sees 100% lockup, but a clutch does. That means two cars with the same final gear, but one auto and one 4 speed, the 4 speed will rev the engine slightly lower at the same highway speed as the auto, since the auto has slippage in the converter.
This is the reason the factory used lower (numerically higher) gears in 4 speed cars. First, they need a little more leverage from takeoff, since there is no torque multiplier (converter). Secondly, since a 4 speed achieves 100% lockup unlike an auto, the engine turns less RPM at the same given speed as the auto, so the 4 speed car can stand a lower ratio gear set. This is why the 3.55 was usually standard in 4 speed cars and the 3.91 and 4.10 were optional. Since your camshaft will be significantly larger than what the factory used in cars with a 4 speed and 3.55s, I would choose the 3.91 gear. Even with the 3.91, you will still be turning less RPM on the highway, than if you had an auto.
