Yeah, that's why I'm not disputing what is being said. My experience deals with a narrower range of lean and rich than what you may have seen in racing engines.
Regarding the flames, I always thought that was because even a proper mixture just doesn't have time to fully burn at the piston speeds seen in racing.

I would have to question if the JK 3.8 would ever get rich enough to cause what the OP is seeing.

I am leaning toward the plugged exhaust (cat), as suggested above.

 

Couldn't timing also be an issue? If the timing is late and the mixture is burning as it's heading out the exhaust valve/manifold instead of mostly in the chamber, that would cause the same condition.

 

I see you have a 08 JK. Are you the original owner? If so don't worry about it you have a lifetime power-train warranty. If it blows you get a brand new motor!

If you are the second owner you need to get this issue looked at by a professional right away! I would definitely take to the dealership and have them force re-flash the ECU back to stock with the Star Scan. This will verify that there is no remnants of a tuner\programmer on the ECU's memory.

 

I am leaning toward the plugged exhaust (cat), as suggested above.[/QUOTE]

A plugged catalytic converter would also be a possible culprit. With a plugged converter, the engine is unable to expell all of the exhaust gases in the cylinder during the exhaust stroke. This leaves oxygen deficient are in the cylinder, which mixes with the fuel air misture coming from the intake valve. This results in a rich mixture that burns slower and will heat the exhaust manifold into a glowing condition.

 

In the OP he says he paid a grand to get manifolds, so I think he's 2nd owner at least.