Okay, so you are trying to change your filter and intake piping then, right? And you are trying to figure out how to deal with the PCV and intake temp sensors, correct? I won't question your motives or comment on the efficacy for changing the filter and piping. I'm sure others will do that plenty.
If you are considering swapping the actual intake manifold just to move the sensor, that would be a ton of work when there are much easier ways to simply mount it on the new piping. Also, there may be a difference in the tune of the PCM to account for a difference in heat soak of the intake manifold vs the piping, but I'm not sure. I suspect there is though. I will also mention I'm unfamiliar with how the newer style intake sensor mounts to the pipe but I stand by my previous comment about there being a way to remount it that is much easier than swapping intake manifolds.
On the PCV/CCV, slapping a filter on the valve cover would work although you would lose the slight vacuum benefit of it being attached at the other end to the intake piping. I doubt that would hurt anything in this application though. What I would be more concerned about is while in theory that would be fine on the street, jeeps are meant to get dirty, wet, muddy, dusty, and attract beautiful women that want to ride topless with you. I could see that being an issue for the open element filter stuck to the top of the valve cover.