After installing the weber kit on my Samurai I have one unaccounted for connection coming from the transmission.  It is a male cylinder with two female connections.  The two wires appear to be black.  I can't find the corresponding female cylinder.

 All my emissions gear has been removed (1986 is exempt in Texas).   Is this an unnecessary connection?

I will look when I get back from Grouse Hunting,
Had too much gear to bring back from the Tomahawk Forestry Shops for our FD to take the Timber Cruiser.
There is the back-up light, neutral Safety switch (Some), and the 5th gear switch. Also the Transfer case has a 4WD switch.
The 5th gear switch is no longer needed for the ECM.
  It will be Monday before I can reply, maybe someone else can check sooner.

CAPT

Sounds like you are talking about either the 5th gear switch, or the back up light switch in the tranny.  Neither are required for the engine to run properly. 

I don't remember, off the top of my head, which switch has which connector end on it (one is male, one is female though).  I guess if your back up lights work, when you put the tranny in reverse (with the key on), then it is the 5th gear switch pigtail, that you are talking about.