Well I'm not in the middle of all you guys to judge exactly what's going on, but if the timing chain idler was broken, your truck would either a) not run at all or b) be making a horrible racket.
But let's say all that was necessary.
Sure a computer could cause this but I doubt it. Computers rarely....RARELY...go bad....if anything, there could be problems in the wiring harness.
As for the variable valve timing issue, I could see that causing a loss of engine power, but not a total misfire in two cylinders.
If they think two cylinders are not firing, then they have to check the coils for those cylinders, and the injectors, and work from there.