I'm putting my engine back in and I can't find the second connector for the air pump. I connected the shorter one but can't find the thats looks like a fuel injector connector. I looked at shoebox's main wire harness picture and I dont see it there either.

 

You don't see it on my engine harness because I never had the AIR pump recall done. That said, I think it is probably part of the chassis forward harness just like the main pump connection is.

 

Whats going to happen if I don't have it plugged in

 

The purge valve for the AIR pump won't work. (I am assuming you are looking for the connector that goes to the valve on the coil stud)

It helps keep moisture out of the pump (the cause of failure of the original pumps).

If you took the connector off, just keep looking. It has to be there.