It turns out the problem was in a somewhat unexpected place.
I pulled the #2 plug, it smelled of gas a bit, but there was spark. Fuel pressure was fine, I could feel the hoses pressurize when the engine was cranking.
I checked the injector resistance at the harness and I couldn't get a reading off any of the injectors. I checked #1 and #2 at the injector and they were both fine. I checked continuity between the harness connector and the #1, #1 and #8 connectors and there was continuity, so I knew the under plenum injector harness was good. I knew at this point the problem was between the battery and the injector harness, since you have to check resistance between the positive post on the battery and the hanress connector. It turned out that the main 25A fuse for the fuel injectors was bad. I don't know what made it pop, but I replaced it and the car is running fine now.
Unfortunately I'm not completely finished. The idle is a bit high and I can hear a hissing noise from the plenum area, so I'm going to have to go hunting for vacuum leaks. At this point I am just glad to have the plenum back on and the car running again. As I found out the hard way: Removing a VH45DE plenum and doing knock sensors is probably the 5th circle of automotive hell.