I have the same issue. Almost feels like the idle shudders or staggers? I too have (fairly) new plugs and wires. Bosch and STI, respectively.

No vacuum leaks or codes. I ordered two new front O2 sensors to see if that helps.

 

Yes it could, depends on if they were gapped right and some engines just do not like some spark plugs.
The NGK's I bought were $2.29 ea. at AutoZone, so for $20 and 30 min of your time you could try them and see what happens.

 

Sounds good, normally if it's vacuum related it will idle a little high. If you have no lights on, the computer thinks everything is rosy. I'd pull the plugs and look at them, make sure they all look like they are burning about the same, they should be a light brown. Make sure your plug wires are good and throw a can of injector cleaner through the system.

 

I would go with Bosch Platinum or NGK plugs. Avoid Autolite and Champion. Did you upgrade to the 8mm wire set? Have you done an induction cleaning? Checked for vacuum leaks?

Eric

 

Good info! Spike555 do you remember what the part number was? Couldnt find a listing for the '03 at auto zone but advanced auto had a couple options in NGK.

 

I have not done an induction cleaning yet, the wires are 8mm. What do the silver crimp flex looking pipes do, that run to the top front of engine? They are probably about 1" in diameter.

 

I might be wrong, but I think the slight roughness is more noticeable on the 4.6 motors.
my brothers 2000 D2 and my other bros 98 D1 both have smooth idles. Both of those engines are using Bosch +4 plugs and 8mm STI wires. My 03 is using the same wires but with NGK Iridium plugs. Plugs maybe?? I assume its the 4.6 motor trait.