unplugged connectors?
 

First under hood right by the intake by the throttle body is an empty connector. No plugs or anything and cant determine where it goes


Next are two connector plugs in the trunk, I plugged one into the antenna which made a weird grinding noise which I'm not sure what to do about so I unplugged it. I couldn't find where the other one went and I don't have keyless entry either

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the one under the hood is egr what year is your car?

the last one is for the power antenna the grinding you hear is the mast gear its prolly broke the other plug is for the keyless entry box that you dont have i believe

According to his profile, his car is a 99. The rest of what you said sounds about right to me.

Hmmm is there is kind of egr delete? I know on my old car that's possible. I didn't see anything to plug in to it.
As for the keyless connector, could I buy the box and hook it up or is it more involved?

Is the check engine light on? Does it even work?

Light doesn't work but I scanned and a knock sensor code comes up

You should be pulling a P1400 code, because that green sensor is the EGRcontrol Solenoid. I just spent the last two weeks dealing with p1400, p1445, and p1447. replaced my vapor canister that was shooting microbits of charcoal all up in my vacuum lines. The ERGC should have a corresponding green connector coming from a harness around where air flow tube is connected to the front upper intake if that makes sense. It's very weird that you are not pulling that code. There is no way for that valve to function if its not getting power.

Bump

I would say your ECU was swapped if you don't have P1400 stored. Examine ECU area to see if it was swapped.