Cap it off and run the SBC in, from the plenum, as you've said. This way, the SBC will get as good a reading as any, as to how much positive and negative pressure, the engine is seeing.
Oh, and if you still have the breather connected to your intake pipe, remove that as well and put a mini filter on the end, then clean as much of the intake track (from MAF to plenum) with petrol). By having the breather output into the intake pipe, you'll be coating your entire intake track with oil mist. This will disrupt air flow and worse still, dilute you fuel mixture, robbing it of octane.
If you do this, I guaruntee your car will feel more responsive !