Ford factory DVD manual questions:

I have a 96 to 99 ford factory SM on DVD i got for my Taurus on Ebay. The manual is FULL of information, but navigating it seems
to be troublesum for me at times. I am trying to resolve some wiring issues in my 97 Taurus with a 96 motor (and 96 motor harness) I know that the 96 motor harness is 95% the same, but NOT exact. The car does run and drive, but won't code scan and runs hot? I can print out the connector (C130) and know what the circuit numbers are and what pins they are. What i cannot figure out how to do is search for a circuit number and have it give me the frames its in or what its is. I can find connector search, or ground search, or component search.
I have found some of the differences, but not all
C130 engine connector: 96 97 pin 5 ckt 347 bk/y pin 5 ckt 914 T/O (AFAICT, 914 is DLC) pin 10 ckt 914 t/o Pin 10 ckt 347 bk/y (347 AC ?)
pin 29 nothing pin 29 ckt 29 Y/W pin 40 nothing pin 40 ckt 570 bk/w pin 41 nothing pin 41 ckt 71 o/lg
What i tried to to is swap C130 pin 5 and 10 (by color code)at the ECM, but that did not fix my no code scan issues. The black/yellow wire on the 96 C130 connector is larger than the one at the ECM, so it must not be the same wire?
If someone could tell me what the circuit numbers are and where they go on the engine, it would be helpful. Or tell me how to acess that info on the DVD. If i knew what the circut was, i could pull up the frame of the device it goes to. I know one of my DLC connectors is swapped, and somehow the A/C plumbing is in the mix too. The car is not flex fuel, and has 3.0L vulcan
I tried to rewire the ECM side because there was better access than the C130 side on top of the transmission. Even though the car is running, i would like to know what the extra C130 pins (29,40,41) are doing or not doing. I have been trying to avoid getting a 97 harness and tearing the top of the motor off to get it on and off.
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