+1 with the wire between the DLC connector and cap....Some models had the outside ran wire so the cap won't get lost.
The two with what appear to be cut wires were for "spare" fuse holders...The cut wire look was more meant to be a "plug" so the electrical weather pack cap seals up better....Along with giving an indication that something electrical was inside such as a fuse..< As just to be more sure, there isn't any other wires connected to the other/bottom side of them Correct?
So when you start your engine the RPM immediately revs to 1600 RPM? First make sure the throttle body is closing via the throttle cable and by looking at the throttle body plates when/by removing the flame arrestor cover.
Then if you don't have a scan tool handy then try following this method to see if there are any fault codes showing up within the ECM....
https://www.youtube.com/watch?v=fSEwwa6D2jM
What year is your engine?