2001 XJ Sport 4.0 165,000 miles
Problem: After rig gets to operating temp and is turned off for less than 30 minutes and restarted again I am having chugging and CEL flashing light. (heat soak?)
Codes Pulled: P0303 Cylinder 3 Misfire, P0203 Injector Circuit/open-Cylinder 3

(unrelated, I think) Changed all major AC components(compressor ate itself, so I had to be thorough) buttoned up the jeep, and heat soak symptoms presented the first time the jeep was at operating temp, turned off, then restarted soon again. I then began to diagnose with the following:
Changed Ignition coil, old coil boots were showing signs of wear. This did not solve the problem.
Plugs looked good, diodes were flat, firing slightly favored one side, but nothing to be concerned with and little to no carbon build up or tracks.
Next, I checked resistance on each injector: 1-12.5ohms, 2-12.7ohms, 3-12.5ohms, 4-14.6ohms, 5-12.5ohms, 6-12.5ohms. I assume this indicates 4 is a bad injector?

Possible other Problems/Solutions:
Fuel Pump, test pressure in fuel rail
CPS, use noid light to diagnose
Wrap fuel rail and injectors with high quality heat shield
Cracked Head, Doubtful, I keep a close eye on oil levels, and had to change coolant when I did ac system. It looked clean; it had more sediment than I would like, but no oil.
Vacuum Leak- I have a slight issue with either a bolt or the gasket for the intake/exhaust manifold that needs to be addressed, but this is a long standing issue.
????

There is a thread where the op wanted to get to the reason of the heat soak, I am looking for something similar. I believe there is something wrong that is causing heat soak, as this has never happened to me before. I do not necessarily want to install fans and cut holes in my hood if I do not have to. I have owned the rig for 50k+ and I take extensive care of it.

Sorry, I know the topic of heat soak has been extensively and exhaustively covered. I have read through seemingly every thread on many different forums on this topic and it almost feels like Im getting more confused on how to diagnose my problem. What I am seeking is some wisdom on a proper "road map" for addressing heat soak as there seems to be many things that can contribute.