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I did some searching on automatic transmission housings a while back. '97 through '99 housings are the same number. '00 is unique, and '01 is unique. I am not sure what makes the housings unique, or if they're not interchangeable. I kind of suspect, after thinking about it for a while, that the changes probably pertain more to the internal functionality of the transmission than the installation into the vehicle. My suspicion is that Honda worked on details of the housing trying to countermeasure some reliability issues of the automatic, and that is why the housings are different. I've notice that the rash of broken automatics seems to be centered around the older models ('97 through '99), so maybe the newer transmissions are the ones to have.
I researched this because I had the opportunity to by a '98 transmission pretty cheap, but I chickened out because of the different part numbers. I just didn't want to be stuck with a transmission that I couldn't install in the car smoothly because of some detail I was unaware of. However, after thinking about it, I think your situation is the best one, where you will install a later transmission into an earlier car. I still don't know about the installation details, but I think you might be getting a better unit.
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