Removing the secondaries will give better power right of idle and make it smoother. Ok If the Carpenter Brutes don't have a O2 senor bung to put it in tuckit up out of the way and uncheck it in Tuneboy or TunECU or buy an eliminator from Dyno jet and leave it turned on, a broad band sensor is used only if you are using a PCV + AT,
with the Jardines I would just put the sensor in the pipe and turn it of in the TuneECU settings