I have an update on this! It's working great!
The issue was the intake runner control, AND fuel injectors. 3 of them. I hooked up a home-brew flow testing rig this weekend and tested all the injectors. The plugged ones (there were 2), gave just a small amount of fuel over the 1 minute test. Maybe 1-2% of the working injectors. Just a few drops. Another injector was ~20% low, and the other three were good. All measuring around the same. I've replaced the 3 injectors, left the butterfly valves that the runner control module actuated open, and it runs like a champ! First time it has run well in over a year!
On a side note, the injectors I got from NAPA were all broken. I got 3 from them, all of them leaked. Some of them quite a bit. I honestly have no idea why they would all leak like that, I was a bit confused. I got 3 from Autozone and they worked great. No problems to report.