I don't think there is any real issue here, just thought this was weird.  I have started my truck the last 2 days with the 3 cylinder high idle engaged.  When I get in the truck my EGT gauge is only reading 50* while the Quad is reading around 560*.  I have both sensors mounted next to each other before they enter the turbo.  When I step on the brake and return to normal idle, both readings equalize.  Does the 3 cylinder idle shut off the first 3 or last 3 cylinders possibly causing this?  I kind of assumed it shut off every other cylinder, 1/3/5 or 2/4/6.  If it matters I am using the moparman switch with the TSB enabled and not the Quad high idle functions.  

Pyro has to be in the rear port. 3 cylinder mode runs on 4, 5, and 6. 1, 2, and 3 are dead. 

 

Firing order: 1, 5, 3, 6, 2, 4

 

Bold numbers fire, and the others are dead. Make sure the high idle on the Quadzilla is disabled.

The Quad idle function is off, I heard it would cause issues since I already had the trucks computer updated to activate it.  So the other probe is just getting air blown on it from the deactivated cylinders, that makes sense.  

With the talk of 3 cylinder idle, I was believing that our 2nd gens can't not run on less than 6 Cylinders just due to how the VP is set up. Is there a way to turn off specific cylinders to check injectors (that may be knocking) and what not?

If you have the very expensive older DRBIII tool or the newer Star Scan Tool you can do cylinder shut downs for injection testing.