There is almost zero change between the LL8 and non-LL8 programs. In fact, the reflash can be (and often is) used whether or not you had the LL8 injector installed.
The reason for the blue CPS timing shift may be related to how the sensors are manufactured, with some folks speculating that the output signal from the sensor is not quite as strong as the black CPS while other think it might just be that the inductor is shifted a little bit in the sensor housing. I don't think anyone really has an answer on that.
Not sure what the cause for your miss is. Can you isolate it to a specific cylinder?
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