Car running like crap

Could it misfiring on the passenger side? Due to a bad spark plug maybe? I think you double-checked yourself the correct firing order, dont you?

2 other things to check. It could be a vaccuum leak. With the engine idling and hood open,stick your head close and listen for any "whistling" noises. Also your mass air meter could be messing up. Take it out and see if there's any nasty build up on the element. It's common to hear of problems after guys re-oil their K&N.(or K&N style)

Maybe you tagged a valve - try doing a compression test on the cylinder bank that's acting up.

From what you described, i would guess 2 things before I would go through a compression test.

First of all what year is the car? Did you gap the plugs? I know these are stupid questions but it will only help you get to the bottom of this problem quicker. Does it have the Coil On Plug (COP) design, of 99 and up? If so I would start by making sure that all your coil packs are snug, lubricated, and fully connected. They have a tendancy to arc out but because there is no whire from a coil pack to the plug, it happens all down in the head. These are a real simple place to start because the car will still run if one is dying out on you and the remainder of the cylinders will carry the load. And often the OBDII will not detect the loss of spark to the plug because there is not a full failure. The low tech way to test and see if a COP has gone bad on you is when you have the rough idle, open the hood and unplug each cop, one at a time and listen to the motor. If you notice no difference than you have found the one that is dying. This just works to help you locate the problem, a little cheaper then bringing it to a tech and paying $60-$100 /hr. for them to locate a problem that the computer says does not exist.

Second, is it hard to keep the car running, and does it sound like your running a big cam in it. If so it may be the Idle Air Control valve (IAC) getting dirty and clogged with carbon. You can test that by removing it from the front of the intake plenum and cleaning it out with carb cleaner and reattaching it. This fix will only work for a little while but it is enough to get you by for a while. You will need to replace it.

Let me know if this was any help, I know i have had what sounds like similar problems and these are the ways that i went about fixing them.

Is it going away after 10 minutes or so? My car was doing this every now and then so I took it to auto zone so they could check my comp. I ended up replacing the fuel injecter pressure sensor,or somehting like that! Just take it up to auto zone and see if your computer shows any codes.