UPDATE: The vacuum hose connections featured in this entry are super wrong! Go here for the correct way to hook up the vacuum hoses.
After a delivery delay due to crappy weather and a busy weekend, I have finally been able to reassemble not just the newly cleaned oil separator but also put the intake manifold back on. The oil separator was just a matter of tightening a couple of bolt and a cable clamp. I’m sure there’s a torque setting for the two that attach it to the block, but I couldn’t find them in any of the literature I have. I tightened it to a point I like to call “not gonna fall off.”
Old and new 
Installed 
Back on the block
The intake manifold gasket went on next, followed by the intake manifold itself. To get it on properly I had to run the fuel injector cables up through the opening in the center and make sure the support bracket underneath was lined up properly. After the manifold was attached and bolted down (again to the point of “not gonna fall off”) I reattached the flame trap hose to the top of the oil separator which is accessible through the two rearmost intakes.
The support bracket 
The injector cables 
The flame trap hose
The final step was connecting the air intake duct between the Mass Airflow Sensor and the throttle. The flame trap was then connected to one of the duct intake nozzles. The other was connected to the front of the Idle Air Control valve, and the other side of the IAC was connected to the intake nozzle on the side of the throttle on the engine side of the throttle butterfly valve. Then the various vacuum lines were connected to their corresponding fittings on the intake and throttle.
The throttle pulley assembly 
Vacuum cables
There are a few connections about which I’m not 100% sure on where to connect them. I’ll have to go back through my photos and parts diagrams to figure it out.
Next stop: fuel rail-ville.