I tested the plenum by plugging the intake off and no vacuum. I know my air hat doesn't sit right and it needs a gasket, but that wouldn't cause a miss would it?
I got a misfire on 2 and 5

 

I do however have a lot of vacuum coming from the pcv but I believe that's normal. I can't feel vacuum on the breather side however I've run out of options with this truck.

 

Disable PCV system, and plug the lines. (both sides of the system) Take off the oil cap, still got vacuum there? Then the plenum is blown. That can be a pretty massive vacuum leak, which will give you all sorts of interesting behavior. Question becomes, how are your ignition parts? Been replaced recently? What plugs are in it? Wires routed per the TSB? LOTS of stuff can cause misfires, from bad plugs, to old O2 sensors.......