You don't need to do anything to them. They will be gone, they are part of the A340H t-case.
FYI- you want an earlier model A340F. I don't know what the year split is, but there are two different reluctor wheels on the tailshafts, a 'two bump' and a 'four prong'. You want the 'two bump', as the tailshaft speed sensor in the A340H has this type. I got a tranny out of a 97 T100 and it's got the two bump. It's possible to modify a four prong but it's a PITA.