First, my disclaimer: I'm not an expert, or a professional mechanic. I do have pretty extensive experience with my Mean Streak, and am myself comfortable working on it, and I'm highly mechanically inclined.
That being said, I was just reading through your description of the issues and your experiences. Here's a couple of notes:
There is only one massive cavity in the tank for fuel. And the fuel pump we have is very good at sucking just about every bit of it out. If you read through some previous threads on the topics of gas/fuel light/gas mileage, you'll find a lot of opinions. My first question related to this: how do you fill your tank? If you were to stick the gas pump nozzle fully into the tank, and only fill till it clicked off, similar to how we fuel an auto/truck, you only have about 1/2 of the fuel the tank is capable of holding. The biggest part of the tank cavity is toward the top. Once the majority of the tank is full, I hold the tip of the nozzle up toward the top and slowly fill until I just have enough room to close the cap. Of course, I only fill like this when I know I'm riding, not just before I park it in the garage.
Second fuel related note: have you verified the "fuel light"-bulb isn't burned out? Have you tried running past the point you think you're low on fuel to see if you can get it to come on?
Ok. Beyond the gas. Try disconnecting your PCIII. You don't have to remove it, just unplug it from the injectors and hook the OEM ones back up. Then go ride it and use that as a comparison to how it's been behaving. If your symptoms don't change, you can eliminate the PCIII as the primary culprit, and start chasing the sensor/smog related issue.