I had a simialar problem last night - very rough idle almost to the point of stalling while waiting at a light. Everything seemed fine before on highway 1/2hour on return from work. Same truck, motor and tuning. This morning no problem to and from work. Same maintenance regarding oil changes etc. Could not see what codes as my programmer out for repair (self induced).
Trucks stock "trouble" light did not come on either.
Would trouble code(s) stay in the computers memory until I get the programmer back?