I can't get enough room above the oil separator to lift it up high enough to remove it. I have removed the throttle body and the IAC motor. I can get good access to it, and can lift it about 1/2".

I think it is being restrained by the wire harness above it. Even when I try to give that more slack, the thickness of the bundle of wires up against the bottom of the intake manifold is keeping me from lifting it up high enough.
The heater hose is also an issue, I think.

It seems very light, so I doubt it is clogged, but now I need to get it out to clean the mounting area.

Any advice here? I'm thinking of pulling out the wire harness.

I had to give up for the night. Hopefully you guys can provide me with some insight.

I agree it seems impossible, but I did manage it by pressing the harness to one side. Don't be tempted to force the box - the plastc lip and lower pipe connection is fragile, and can break and bits fall into the sump.
I have an idea I cut off the lug on top for securing the harness, to get a bit more clearance.
Possibly slitting the harness plastic cover to let the individual wires splay out more would help, and then tape it up afterwards.

What lug on top? On top of what?

My separator box has a vertical plastic lug on the top, with a metal clip to take a screw holding the wiring harness. At one point the lug seemed to be the thing catching on the underside of the manifold so I just cut it off. The harness does not need any particular securing, it is a struggle enough to move it even a small distance for clearance.

Thanks for the encouragement. I'm glad to hear that it can be done without removing the intake manifold.