I had to disconnect all these harnesses when changing the front valve cover. The harness outlined in red only had 3 pins, while all the others had 4 pins. I'm wondering if that's normal or if something broke off. Are all these harnesses for the oxygen sensors?

 

I think that it is supposed to have 3 pins and it is an o2 sensor plug.
As

 

You mean crank sensor?

 

In the 2001 its an ECM plug.
CKPS runs through it back to the ECM.

There are four 02 sensor plugs. One by the P/S hose and three more up front.

The fourth(green) is not an 02 sensor connector!

 

It goes to the crank sensor and it is 3 wire.
You just have to look at the number of wires in the harness to know how many pins it will have in the plug.

The light blue one is the primary o2 for the front bank and the two in the center are the heated secondary o2 sensors. The primary for the rear bank plugs in near the PS pump.