Can anyone tell me the depth that the output shaft seal (both sides if they are different) needs to be below the top of the bore? Replacing mine and they are different depths as well as one is not flat in the bore.

Yes - they were leaking

Should they be flush?

Any help would be appreciated.

 

iirc there should be a lip on the inside that they bottom out on. if not i would just got flush to the outside.