I hope when the thermostat was replaced all the air was burped out and only HOAT anti-freeze was used?
What exactly are the codes you are getting?
What plugs did you replace with...normal copper NGKs are what I see recommended most but I do not use plugs so would not know.
Misfire on a cylinder could be caused by bad fuel injector. You sure you are counting the cylinders correctly?
Could also be caused by a bad Crankshaft Position Sensor or Camshaft position Sensor....hopefully codes will show this up.
You need to measure the wiring coming from the PCM to each coil and injector...check for continuity of the leads, resistance of the coil/injector and very important that none of the leads register any form of a short to ground.....hope you have a good Multimeter!
The trouble with having a short to ground...lets say on cylinder 6 coil....is that it will blow that section of the PCM so even if you find and repair the short the PCM will have that particular Power Transistor blown and calls for a PCM repair/replace.
You can download the 2003 KJ Service Manual here if you do not have it already....tells you what to do about the codes and includes circuit diagrams.