Can't read CEL

[eggsalads]

Mr fixkick, thank you for answering so thoroughly, I did leave out a lot of info, sorry about that.
This Tracker has the 8v. The sticker under the hood does not say California. 
The DLC connector has 4 pins. I incorrectly referred to the pins with numbers 2 + 3 when I meant B + C.  

I found the NAG switch. I took apart the gauge cluster and removed the NAG switch connector (which had pink and green wires). I tried to read the codes again with the NAG switch removed but still do not see any flashing in any state -- ignition on, cranking, or engine running. I am using a piece of wire. The light is still on, so I assume then we know it's a real code and not a NAG light coming on. What am I missing sir?


Also, there are a few wires going nowhere next to the DLC connector... What is the single wire (orange) pictured far right in the photo I attached? I found The temp gauge sender located under the thermostat was broken off. I replaced it and wired it up but I can't figure out where the heck it is supposed to go.

looks like , car has calif hood on fed body, first.
the CEL glows steady,
4pin B to C ( what pins you call them is no matter ) what matter is the index clip in side, as reference point,
your are not missing anything I can see.
those extra wires and plugs are, for AC options,, 2door car has  no rear wiper and extra wires for that.

, the ECU sees to have bad CAPS, if the are bad the CEL Lamps goes dead or stuck on, or blinks are wild.

the DLC has new a rubber cap, i  , the wire colors are what mater. Blue-yellow   (blue with yellow stripe, ignore color dots when seen)

the Blue-yellow  wire found is jumper to ground and CEL flashes out codes, 12 = good.

So, bad ECU? I assume I must remove it and look inside to see if the caps are leaking? 
I really just want the tracker to run right. I feel as though it is an ECT issue since I have the temp gauge not working also. Thoughts? The temp gauge sender was broken. I replaced it but now I don't know where to plug it into?