Great questions that I wish I had answers to. I don't have a fuel pressure gauge to check that. I might need to invest in one.
As far as the PO, I really have no idea what has been done. I'm going way out on a limb here and assume it's bone stock. I only say that because of the Carfax report. The PO was a stickler for maintenance and he used the dealership for things like oil changes. The interior was also well kept. Maybe he did that for warranty reasons or maybe he was a guy that doesn't like to mess with things. To me that says the PO was a guy that valued the car, and probably didn't want to beat on it like a typical Cobalt owner. I really have no idea though.
I'm guessing there is really no quick and easy way to peek into an ECM and see if things are stock or not? I don't have access to an HP tuner. I would like to do a reflash, but I'm worried about it breaking things even more based on what the dealer was telling me.
I'm still in the process of eliminating mechanical problems like O2 sensors, fuel pressure, etc. I'll go the tune route if I can't figure out why my LTFTs are so out of whack.