Alright! Here is the list of repairs I have completed in the last several months:
1) replaced plugs and wires (just because I had never changed them and the car had nearly 120K miles)
2) replaced plugs because I tightend 2 of them too much and they cracked
3) replaced LIM gasket as well as coolant elbows, valve cover gaskets, and 02 sensor

Everything is going great except I still have a misfire!!! I do not know what is going on!! I have checked the plugs and wires, and even checked to see if #6 is touching the 02 sensor, it is not. I bought good wires from NAPA and they seem to be ok. When I took it to the shop last week to fix a vaccuum leak, the got a code that had something to do with the EGR valve and another time they got a code for the CAT. Would either of those create a misfire? I am very puzzeled. To tell you the truth. I started to have the misfire problems after I changed the plugs but I could swear they are ok. One other thing, when you give it gas, it initially is worse than just at normal idle. Then once you maintain speed, the miss seems to be gone. Could I have a bad coil? Could a really bad miss damage the coils? I did have a problem where I burned up a plug because I was stupid and ran it too hard while the motor was running lean I hope someone can answer this rant for me!

I'm going with plugs here. You can not crack a plug by overtightening. What you do is use a non-cushioned plug socket and at the same time do not keep the plug socket "square" on the plug as you apply torque. What happens is you crack the ceramic insulator. If you did that to 2 plugs I'm betting you may have cracked others but they did not "give way" so you did not notice.

Try a whole 'nuther set and get yourself a new plug socket. Also make sure your plug boots make clean contact with the plugs when you push them back on. I always use a dab of dielectric silicone grease on the tip of each plug before I install the boots. This will insure good contact. While you are at it put some dielectric on the distributor "****", or should I have said nipples.

A clogged Cat can cause a misfire... whats your top end performance like?

define 'top end performancel' more clearly. I know it misfires very bad if you really get on it or are going over 110.

Top end is the higher half of the rpm range, from what you describe it'* not good. WOT runs to 110 probably not a good idea until you find your problem. Is your service engine light on? in your first post you said you ruined a plug from running lean. did you run a compression test ? I would seriously ivestigate further damage to the cylider you pulled the ruined plug from, if you didnt allready that is.

Yeah, I ran over 110 once since all of this. I know, it was not smart I have not done a compression test. One simple thing maybe, I have pulled the plugs a few times since I reinstalled them and I have not put any of the dielectric(?) grease on them. Could that cause a slight misfire? Just a thought. Also, my state does not check for emissions, could I run a straight pipe? Again, just a thought.

I am no expert but once I had a similar problem as to the sometimes egr code being set off and tried replacing the egr valve but still had the code come up upon further investigation the problem was being caused by my pcv valve because the o ring was not put back on it upon replaement and it caused excessive vacume being caused by it not being there and it also seemed to cause a miss fire.

Also if it was a missfire wouldn't that set a code to????You stated that you are getting codes for egr and cat so theres a start.

My cat was plugged to at one time and under wot it seemed to missfire until I replaced it.And yes you can run with out a cat as long as you use a o2 simulator for the rear o2 sensor.Otherwise you will get another code.But I am not sure if you loose boost because these cars seem to like alot of back pressure.

Also if it is your egr valve I wouldnt waste the money for a new one if you remove it and clean the pin that is supposed to move freely with some wd40 or carb cleaner and get it to move freely again,that is what is usually the problem with most egr valves from my experience.

I might also suspect the Ignition Control Module; that'* what your coil packs mount to. :?

Sounds like you have the exact same problem I had when I first bought mine a month ago. Mine needed new plugs and wires just because they were the originals and there was an abrasion on wire 3... so changed all the plugs and wires and it turned out it was a bad coil. I'm thinking you've got a coil problem also.

I wouldn't think so, 99% of all misfires are plug or plug wire related. An ICM issue typically is seen as erratic behavior or a no start.

Since two of the plugs were cracked upon original install, I'd be inclined to aim for another set and being careful to put them in reasonably (not so much force with an eye for detail on angles). Also plug selection is something to consider. Bosch has a bad failure rate in our waste spark systems, for that reason is not recommended. AC Delco, Autolite and NGK plugs have good reliability from our experiences.