i have an 06 mega cab 4x4 auto, running rough so everyone told me it was injectors , so i dropped 3k on reman units. thought it fixed the problem until the engine warmed up to operating temp. changed injector wiring harness/gasket still doin the thing. omhed them out and came up with .50 ohm on the injectors. also replaced the whole engine wiriing harness still doin the same stuff warm up and run rough misfire, getting codes 2149, 0251, 0606, 0088. bout to go insane with this truck

 

Have you checked rail pressure?

0606 is a ECM hardware issue. Have you cleared the codes?

 

yea rail pressure checked out and Lift pump pressure checks out to and yea the codes are cleared they come back when the truck hits operating temps

 

Then I think you might be looking at a new ECM, which sucks.

 

Make sure the rail pressure sensor is not plugged in backwards. Is very easy to do.. Don't ask me how I know.

meaning the connector from harness onto the sensor being backwards.

 

Been there, done that, it sucks! With the issues you are having I would check that connection as well.