I've made some progress! The PMO ITBs, fuel lines, rails, vacuum hoses, DBW motor, and electric pedal are all installed. Now, I just need to wire the COPs, injectors, fuel pressure sensor, air temp sensor, tachometer, and a few other components.
For anyone attempting this, here's a tip: don't do what I did. I dropped the engine to make installing everything easier, which worked well. I placed the Nexus R3 under the passenger seat, and I'm happy with that location. I routed the wiring harness into the engine compartment while the engine was out of the car. Doing this with the engine in place would have been a nightmare, if not impossible, since the harness is over an inch in diameter and quite unwieldy.
After reinstalling the engine, I reconnected everything—clutch, axles, etc. That was a big mistake. I should have supported the engine on stands, figured out all the wire routing and lengths, then dropped the engine again to pull the harness and make all the terminations on my workbench. Doing these terminations in the car is backbreaking and time-consuming.
I'm struggling a bit with the terminations. I'm never quite sure how much slack to leave so I'm erring on the side of caution. I wish I'd bought connectors with boots for the wiring.