We are trying to avoid the tail shaft swap if at all possible but thanks for the heads up we have been messin with the wireing all night and just decided to call it a night hopefully tomorrow we can figure something out. Split years suck!
You don't have to swap the shaft, just a rotor snap-ringed onto it and the metal housing that goes around it, plus sensor. Yeah, it's going to be a pain in the arse to do now that the transmission is installed in the Jeep.
You COULD install the 98 TCU, but I see two possible snags -
* the 98 TCU may get really unhappy about trying to talk to the 97 ECU. I don't think it will, but it may.
* the 98 TCU will expect the signal from the input speed sensor as well (the one right up near the shift selector cable) so you may have to run one or two wires from the transmission wiring harness connector by the tranny dipstick tube to the TCU under the steering column. It's only like 12 feet of wire, if you don't mind doing it, go for it. You will want the connector for the 98 TCU at the very least, since you'll need to pull one or two pins out of it and insert them into the 97 TCU's connector in the right cavities, then plug the 98 TCU into it. This may be more difficult than swapping the entire engine compartment wiring harness and dash wiring harness, but I don't think it will be.
If you can verify that the 98 TCU will peacefully coexist with the 97 ECU, this gets a lot simpler. Adding the wiring for the input speed sensor should not cause problems with using a 97 TCU and a 1pps (97-down) output speed sensor + rotor in the future AFAIK, so it's worth a try I guess.
A 97 FSM and a 98 FSM will GREATLY aid you in doing this wiring. I don't know the wire colors offhand for the input speed sensor, else I'd post them up for you.