Ok, so I got my AutoCal, went into the software, and proceeded to complete what I thought was an ethanol percentage reset and a idle relearn. The issues persisted all through the drive home from Nevada yesterday. Today, when I got into the truck, it wouldn't start. It would crank and crank, but wouldn't start..like it wasn't getting fuel. I frantically e-mail Justin (again) asking his advice.
He promptly e-mailed me back basically saying "dude...the log you sent doesn't show that the ethanol corrections have been made. Did you do it correctly?"
I read through the instructions again, and realized that while I selected the correct action in the software, I didn't actually complete it. I once again hooked my computer up, repeated the ethanol percentage correction and idle relearn (correctly this time), and the truck fired RIGHT up. No sputtering, no hesitation, everything running great. How it was explained to me was that when the intake tube came off, the extra rush of unmetered air really screwed up the AFR and made the truck think it had E85 in the tank instead of gasoline. Even after putting the tube back on, without correcting the ethanol percentage in the computer, the truck was flooding itself trying to get the fueling correct. That's why it had been sputtering at startup. Today it finally got to the point that it wouldn't run at all because it was injecting so much fuel during startup.
I'll report back if anything changes but at this point, I'm fairly confident that the problem is SOLVED.
About damn time!