Plugs and wires (check) - replaced both
How did the plugs look when you replaced them, any fouled? - Plugs looked worn but no fouling
Are any coil posts corroded or rusty looking? - Coils seem to be OK, clean connections, proper resistance and spark seems strong
Are any plug wires touching the O2 sensor wiring? - Not touching, there is probably 1 inch in between one plug wire and the 02
What temp is the PCM coolant temp sensor reading? (the dash is a different sensor and can not be relied upon) - Not sure how to check this??
What grade of fuel are you using? - 93 octane
Does the catalytic converter rattle? - Don't believe so, would't I be able to hear it?
Are there any other odd things happening that you believe to be unrelated that you didn't mention? - Well the dash cluster goes in and out, and I have the typical problem with the engine getting starved for fuel when under 1/4 tank of gas which I believe is because a fuel tank defect?
How much fuel pressure does the vehicle have? - Don't have the tester yet
Is the fuel pump excessively loud (aka can you hear it)? - I can hear it switch on for 2 seconds when turning the ignition but I wouldn't call it excessively loud
Did you check all vacuum hoses including the ones under the airbox at the charcoal canister? - No going to do this
Do your exhaust manifolds have cracks in them? - Not that I can tell, will take a look

Thanks for the reply btw Billboost - currently have no ses light or codes stored.

I would do a compression check to see if there is a burned exhaust valve

I had a similar problem with misfire and rough idle. It turned out to be the NEW spark plug wires I installed. They were electrically in spec, but they just didn't work. I upgraded to top quality wires with a resistance much lower than the spec and it worked. Pep Boys even gave me my money back.

I have since learned that the reason is this type of V-6 uses a "waste spark ignition" which sparks both an exhausting cylinder and a compression cyclinder simultaneously. The carbon in the exhaust enhances the spark on the power cylinder. It takes a beefy plug cable to work right. If it doesn't than the weak spark leaves unburnt fuel in the exhaust which backfires and causes a really rough idle. I used a scanner to check all of the sensors, O2, MAF, coils, you name it. In the end it was some crappy Bosch plugs and cables. Use Delco plugs and high performance plug wires and see what happens.

Thanks for the info DrDave - something to consider. When I got the plugs/wires replaced I did ask for OEM stuff so I didnt think this would be a problem. I also heard that lowering resistance wires can be bad if the engine isnt speced for it... any truth to that?

I'm about ready to throw in the towel and take it to the dealer to have it hooked up to the computer. I could do most of the test myself but dont have all the right tools to test the compression, fuel lines etc.

I think I'm gonna seafoam it first to clear out the vac lines maybe that will help

Although a lot of possible causes have already been discussed (and there are LOTS of possible causes for a rough idle), it could also be caused by other things that I didn't see mentioned - a vacuum leak, dirty throttle body, plugged/dirty EGR valve, PCV valve, or fuel pressure regulator.

With the exception of the IAC valve, if there was a problem with most of the other items already discussed, there'd most likely be other symptoms.

OH, and it'd also be a good idea to check the boost actuator (make sure that it holds vacuum), and and also check to make sure that the small rubber vaccum line that connects the boost solenoid to the boost actuator isn't collapsing when the engine is warm. Believe it or not, that vacuum line was doing that on my '92 and my '93 so I replaced them.

Thanks billha, I will check into that - is there an easy way to check for vacuum on the actuator?

I did check the vac lines and they felt good, but I will check em again when the engine is warm.

The best way to check the boost actuator (or any vacuum device or hose) is with a vacuum gun. If you don't have one, you can do it the old-fashioned way and put a clean piece of vacuum tubing on the fitting and suck the tubing and put the open end of the tubing on your tongue and make sure that the suction remains present for 10 seconds or more...but that may not tell you if there'* a very slow vacuum leak.