Your #3 plug sounds fine. Your #5 will be black from miss firing. Sounds like it's the plug.

 

Update2: after switching the plugs 3to5 I headed home. Something on the way home misfiring when I got on the gas a bit. Get home scan and it's still cylinder 5. Didn't get a chance to buy the Lucas so will try to get it tomorrow if I get a chance. At this point I'm leaning towards the injector being fouled up or going bad.
I don't know if that makes sense but not sure if injectors will just die or gradually die.

 

Have you tried switching your plug wire? Before you get a new injector take the #5 out and switch it with your #3 to see if it changes.

 

So I finally had some time and ok weather to get under the hood and try some things. Luckily I didn't need to drive all week.
So I took 3800's suggestion and swapped the coil packs 2/5 to location 6/3.
Checked to make sure had no codes and hit the road.
Punched it misfire, pulled over checked the code and sure enough cylinder 3 was the one that misfired.
Looks like the coil pack is the culprit.
I was looking to replace all of them just to know all are new with:

Standard Motor Products DR39 - Standard Motor Ignition Coils - Overview - SummitRacing.com

 

So they are all replaced now? You get the ones you listed or you get msd coils?

 

I had the same problem a couple summers ago. During a 90+ degree day I was on my way to work when my car started running really bad, first the engine light came on, then started flashing while trying to merge on the interstate. I didn't know what was wrong, so I parked it a got a different ride to work. Later drove it after cool and ran fine till warm again. Long story short it was a bad coil pack. Running great since! Glad to hear you figured it out.

 

3800: I have not replaced yet, just did this today. I am thinking about getting the standard that I put up the link for. I would prefer MSD but when I called Summit they said they don't believe I can use the MSD #8224 for my 2001 3.8 and when you search by make, model, engine size they don't come up.

Vanquishfist: I am very happy to have finally figured out whats been going on and glad to here that yours is running well. I can't wait to get Midnight running right again.

 

The msd for the camaros don't come up for all years but all 3.8l have the same coil packs and ignition module so they will work.

 

I just looked up your car on the msd website and it's the 8224 that you need.
http://www.msdignition.com/appguidedomestic.aspx

 

3800: that's what I thought too then when I called Summit's tech line they said they didn't think they would work. Thanks for looking that up I'm definitely going with the MSD's over those standards.