UPDATE: The tuner who originally did the work is very hard to get a hold of. He surprised me last night by answering my texts. He's thinking that his tune is still in there, and what was flashed on top of it by the dealer was an update, and that's why it's a ragged mess. So the problem is very likely more 'software' than 'hardware'.
Long story as short as possible:
Before the dealer did this, I'd had upgraded injectors with a three-port solenoid and the car was tuned to that. When the dealer flashed the ECU, in order to be able to drive it, I had them put the stock injectors back in, hoping that would fix the problem. It's drivable this way, but the CEL is probably still coming on because Franken-tune is wigging out at the fact that I still have the three port solenoid. So it's likely never going to be happy with the stock injectors.
The good news is, I managed to get the name of a reputable tuner in this area who can put my modified injectors back in and re-tune me. I was happy with my STI the way it was, so I just want to get back to that.
The bad news is, he may not be available before two weeks from now.
I'm going to get that Tactrix that you guys have suggested here. I'll be using that to make backups or take logs in future. And if this guy really does a good job, I'll share his name here for anyone in the Tampa area who needs a tune.
Let me know if you have any questions or think I missed anything. I'll update this thread as things change.