Here's my understanding from some Darin Morgan videos: Intake manifold for dry flow in a MPFI system would be smooth. Downstream of the injectors needs to be rough, 60 grit or rougher. The interesting thing is that upstream of the injectors (for some distance I can't remember) needs to be rough as well. This is because flow is not always in one direction.
For wet flow intake manifolds and runners, 36 grit. For heads, 60 grit or rougher. As velocity goes up, surfaces can be smoother. Since intake manifolds/runners are usually lower velocity than head ports, go with rougher texture.