I'm doing a 4L80E swap and got the speartech harness. I didn't even notice until after I mounted the transmission that the second connector has nothing to plug into. There is the main control connector and the 2 little ones, I'm referring to the rear small one. The front sensor plugged in but what does the rear one do?

 

You have two sensors on a 4l80e. The front one is a turbine speed sensor and the rear one is an output speed sensor. Good luck, Vince.

 

It doesn't look like there's a sensor there, it just looks like there is a plug.

 

Hope that trans didn't come out of a 4x4.
4x4 4L80E's usually have the rear connector on the transfer case, the rear hole on the trans is plugged. Thats not too bad, the problem is there is not usually a reluctor wheel for the rear sensor.
Usually you need to put the reluctor wheel on when you swap the output shaft.