Well just to update, so far so good. The jeep passed emmisions, today with no problem at all. Thanks again Kastein for the help. I was on the edge of swapping in a 98+ transmission cause I couldn't figure it out. So you saved me a lot of work there!
But just to sum up everything I did, I used the 98+ wire harness and cut and spliced it to work with all of the 97 sensors. There wasn't much involved with that because the wires are all the same colors. But leave the plug for the ISS (Input Speed Sensor) alone and just zip tie it out of the way. The only reason for using the 98+ transmission harness is because the plug where it hooks in to the rest of the harness near the dipstick is different. Also used the new CPS (crank position sensor). Had to ground the one wire on the OSS (output shaft speed sensor).
Also replaced the 98+ TCM (Transmission Control Module) with the 97 TCM. (This required trimming a bit of plastic on the harness plug which doesn't hurt the plug in any way.)
Everything is working like it should on it now.
Hope this helps for anyone else wanting to try this.
But just to sum up everything I did, I used the 98+ wire harness and cut and spliced it to work with all of the 97 sensors. There wasn't much involved with that because the wires are all the same colors. But leave the plug for the ISS (Input Speed Sensor) alone and just zip tie it out of the way. The only reason for using the 98+ transmission harness is because the plug where it hooks in to the rest of the harness near the dipstick is different. Also used the new CPS (crank position sensor). Had to ground the one wire on the OSS (output shaft speed sensor).
Also replaced the 98+ TCM (Transmission Control Module) with the 97 TCM. (This required trimming a bit of plastic on the harness plug which doesn't hurt the plug in any way.)
Everything is working like it should on it now.
Hope this helps for anyone else wanting to try this.