After repairing the knock sensor, I reinstalled the air pump system (not pictured.) Even though I've bypassed the system and it should never activate, I replaced the air hose that I cut off earlier. Part number is 17342-50180, picked it up off Amazon here:
Amazon.com: Toyota 17342-50180 Air Injection System Hose : Automotive
Next, prepare the pigtail connector by putting some heatshrink on so I know what wire goes where:
Solder and shrink it up:
Put some wire loom around it:
Tape it up. Didn't armor these wires like the knock sensor, I got tired. You can see the new air hose on the left:
Last, buttoned it all up by reversing the steps to install the intake manifold. Replaced the intake manifold gasket. Noticed that 7(!) out of the 8 fuel injectors were missing the lower gasket where the injector mates up to the manifold, so replaced all 8. Part number 23291-41010.
First start failed, because I didn't hook up the main wiring harness behind the intake manifold - oops! Second start (without airbox or vacuum lines hooked up) fired, but died instantly. Third start with everything hooked up was good! Cleared the codes using an OBD2 tool and I've been good to go.
Hope this helps someone searching this issue in the future. Cheers to all contributing good info to the forums!