What is the difference between 1999 and 2000 PCM harness

[Liv4Drums]

I have a 1999 WJ Limited 4.7 non-HO that has a decent body and only 50,000mi on the transmission and transfer case and a 2000 WJ Limited 4.7 non-HO from the rustbelt with a trashed body. I am replacing the complete wiring harnesses, interior, dash, HVAC and all electronics of the 1999 with the 2000 harnesses, interior, dash, HVAC and electronics. I am doing a complete swap of wiring harness due to the 1999 wiring harness being hacked-up quite badly. I am almost done with the complete 4.7 engine rebuild but before I reinstall the rebuilt motor, I am wanting to paint the engine compartment and finish up the wiring harness installation.

My question is that I have noticed a difference between the 1999 and 2000 PCM harnesses. I have included photos of the differences between the two. The PCM harness out of the 2000 has an additional connector (indicated by red tape) that goes to the transmission? but I am not sure or remember to exactly where. I have read somewhere that there are differences between the two transmissions electronically (1999 and 2000). Is this additional plug part of the difference between the two? Can someone explain exactly what the differences are between the 1999 and 2000 transmissions and what will have to be modified in order to utilize the 2000 harnesses?
I am hoping someone will have an answer/solution to this dilemma.
Thanks for your reply.