You keep the upper piece of the plenum when replacing the Butterfly portion of the intake. Here is someone else's write-up. It's how I did mine. http://www.4x4wire.com/mitsubishi/tech/lower_plenum/
And as far as noticing a miss... mine did it the most under load when cold or on highway when under load. Just driving around town it would hardly do it. Over time it got worse. This truck can manage a lot of leakage bfore it's noticed.
These trucks are notorius for intake issues- the way the were bolted down is not great. Hope this helps you. I still think mine has tiny leak but it is the best it's ever been.