The intake manifold can get a little oily inside because the PCV system pulls oil fumes into the intake manifold. It shouldn't affect the performance of the MAP sensor.
One thing I did notice on your photo of the MAP sensor connector, is that it is gray. The throttle position sensor (TPS) on the throttle body has a very similar connector, same basic shape and three wires. According to the FSM, the connector on the TPS is gray, and the connector on the MAP sensor is black. Is the connector on your TPS black? Is the wiring long enough on both connectors to reach the other sensor? I'm thinking they may be swapped, which would really confuse the PCM.
One thing I did notice on your photo of the MAP sensor connector, is that it is gray. The throttle position sensor (TPS) on the throttle body has a very similar connector, same basic shape and three wires. According to the FSM, the connector on the TPS is gray, and the connector on the MAP sensor is black. Is the connector on your TPS black? Is the wiring long enough on both connectors to reach the other sensor? I'm thinking they may be swapped, which would really confuse the PCM.