Japanese engine and transmission swap.

I'm restoring a 1999 Honda Accord Sedan. I decided to purchase a new engine and transmission from Japan. I'm having a problem with the transmission, I'm hearing a clanking noise when I put it in gear although it still works. I've been told that the computer is different between Japanese and American models, and that I need to do something with the sensors. Can anyone please provide more detailed information as to what I need to do. Thank you.