I recently bought a 94 Eclipse GS that needed a new engine, so i replaced it and now im having electrical issues. it has to be a ground problem but when i was searching around i noticed 3 plug ins on the harness by the firewall that the male end wasnt going anywhere and im wondering if it is my issue

 

That picture is a little blurry, but if you are referring to the plug on the right facing down, that one is used to adjust the engine timing, so it has no connections, that's the way it is.