Did you also replace the boot and use some dielectric grease? When was the last time you replaced the plugs? What brand did you use? Also, have you completely removed the TB and cleaned it lately?
Is this a forced induction app? Your AFR looks awfully rich for NA, and your TPS is awfully high for an I5, especially idleing at 550-650.
Mine will do something similar sometimes at the first start up after loading a tune, and then that's it. I still haven't tracked down the cause. Just figured it was a bug of some sort.
If it's an ongoing issue, you may want to do a leakdown test- there was a TSB on the cylinder heads in the 2.8 and 3.5's in regards to valve seats. P0300 was the initial indicator, but typically it was a few cylinders IIRC.
I don't know if it's in this thread, but it was extended each year to include 06, 07, etc...
http://coloradofans.com/forums/viewt...hlight=misfire