"If you dont want to hook it up ATLEAST cap it totally off or remove the other side and put two air filters on the valve covers." Sorry JD, not sure what you mean here. I have my PCV system installed as designed with the breather tube (what I called "fresh air tube") hooked up downstream of the MAF connecting the valve cover and the intake tube.
Not to keep the PCV debate going (this will be my last mention of it, so as not to go off way too far from the initial thread), but that tube downstream of the MAF to the valve cover is indeed a fresh air inlet to help collect blow by gases in the crankcase, which are then routed to the intake manifold. Yes there is vacuum in the intake tube, but manifold vacuum is much larger than intake tube vacuum (in most cases, depending on the position of the throttle plate) and at idle is enough to take a little bit of air from the intake tube through the crankcase. This is how the PCV system is described in the Haynes manual, and here are a few other sources saying the same thing:
http://www.machinerylubrication.com/Read/234/pcv-system
http://auto.howstuffworks.com/positive-crankcase-ventilation-system.htm
http://www.aa1car.com/library/pcv.htm
Now I did come across some literature that described a similar PCV system to what you described, but I think all of the later model vehicles PCV systems work as described in the Haynes manual.
OK, I'm done with PCV. Not trying to be condescending or a jerk, but I'm gonna get back to the idle issue.
I got my ICM in the mail yesterday (wasn't expecting that). And I also swung by NAPA and got a Crank Position sensor just for kicks and grins. I installed the ICM first, fired it up (did not reset the computer) and waited. About two minutes in, still running rough. So I replaced the CPS, fired it up and waited. Waited and waited some more. All of a sudden, she was smooth. I would put it in gear, and she would hover around 850-900 RPM. So I took it for a drive. Everytime I came to a stop it was like a dream. PERFECT, so I got back home and parked it, then I disconnected the battery to clear the memory. Fired it up and it was back to being rough.
So I let it sit for a few minutes, all of a sudden it was like a switch was thrown and it was smooth again. Put it in gear, and all was well. Great, the computer just had to figure itself out...or so I thought.
So when I went to work this AM, fired it up, and it was rough again. Even after driving a bit, she never settled out to how she was last night (last night was BUTTER before I came back inside). I thought it may have to relearn cold settings or something, but once it warmed up it wasn't how it should be.
One thing I will note though, is that last night during the "rough" spells, I did disconnect my MAFS, and she idled like a dream, and when I reconnected it it went back to acting up. So I wonder if somehow last night in playing around with that, the MAFS acted fine just enough for me to cut the truck off and go inside, and now it's acting up again? I could have swore that when I disconnected the MAFS previously, it bogged, but not last night.
So on my drive home today I'll see what happens. Once I get close to the house, I'm gonna stop and disconnect the MAFS, then drive easy the rest of the way home and see how she is.