Is you Knock sensor taking performance down for the count?

[XfireZ51]

The Service ASR light will come on when in ALDL mode. So if you connected your scan tool, you'll see the light. The Service Ride Control will light if you've started the car 3 times without moving it.
Does the vacuum pump come on when you turn ignition "ON"? It's in the front passenger side by the coolant overflow "bottle". It should only run for a few seconds. If it continues, there's a vacuum leak and will affect secondary operation. With your scan tool I would check all sensor values with ignition "ON" making sure they are within range, like TPS, MAP etc. Check hoses like the PCV connections and the MAP sensor.
Have you pulled plugs and how did they look?
I know this sounds basic, but from our perspective here, it helps to understand the baseline condition of the car before speculating on what's going on.