I just went through this today actually. I swapped my automatic transmission on my ‘99 Limited to a 5-speed a couple of weeks ago, but when I tried the new manual transmission ECU, it would not start. After some quick diagnosing I found it to be my immobilizer.

I researched for about a week on how to get the new ECU to work with my keys. I called a local locksmith, explained the situation to him, and he claimed he could get my new ECU to work.

I met with him today. He took my Auto ECU first, clipped the EEPROM reader onto my IC900 chip, and then he was able to find the immobilizer codes after ~5 minutes of experimenting with different EEPROM scanner protocols. Honestly I’m glad I didn’t try doing this myself because it seemed very complicated just to be able to read the values stored on the chip. He copied the values on my chip, and pasted those values on my manual ECU IC900 chip, so all my keys work with the new manual ECU without needing to program any keys. He charged $160 which I thought was a fair price.

Props to you OP for figuring this out yourself! I think this is some pretty complex stuff and I’m an engineer so that’s saying something.