upper intake manifold

I believe box upper intakes don't keep much vacuum, so you might need a vacuum booster in order to help with the vacuum assist brakes. Also, changing the runner length has an affect on the engine's torque range. I'm not sure how switching to the box upper will affect this but I'm sure there will be a change. It really depends on what other parts you will use to compliment your combo.
 
The F cam is pretty good about vaccum I believe. It doesn't have a whole heap of overlap if I remember correctly.

I don't know how I feel about the box intake, there is one for a stock lower, and one for a gt40 lower. A box intake on a stock lower is about as useless as it gets. The stock lower sucks and doesn't flow, it doesn't matter how big you go before it, because the stock lower is the bottleneck, not the upper.

On a gt40, you're better off, but I really don't know how well the gt40 lower flows.

Box intakes are really meant for poweradders or really high rpms. If you're building a 8k rpm+ NA motor or a turbo motor I could understand a box upper. Outside of that it's not going to do anything for you that any normal upper intake manifold would.

The fact that it's a box shouldn't have any effect on vaccum.