It don't matter if you had ATF in there or not. ATF is actually a good detergent to clean the internals out but having too much can cause excessive wear because the gears are not getting the proper lubrication.

I guess you never use ATF in your engine before huh? You can use it if your engine is noisy or getting old. It cleans out the internals very good. Most use Sea foam but ATF works just as good. It's know that mechanics use a mixture of ATF and MTF in Honda's and other cars that use engine oil in their trannies to make things smoother.

Anyways back to the point, since you found the problem then just replace it with Honda MTF or with the Penns Oil Syncromesh or with regular 10w30 motor oil which ever you want to use. I would go with the Syncromesh IMO.

Make sure you got the correct Axle seals for your axle in your tranny.