We have a MS2A-E reverse gear. In our case the engine
rotates clockwise (looking at front) and prop is right handed (rotates clockwise looking from rear) so box reverses the shaft rotation. Looking at the exploded diagram of the box I believe that means that in our case the lower gear of the gear set that engage the output gear is the forward driving one (if I have done the mental gymnastics correctly
It should be easy enough to check for sure if the shaft rotation is reversed by manually barring the engine over clockwise (I use a socket on the front pulley nut) with the box in gear and observing the box output side rotation - assuming one is at the boat
and I am assuming that the clutch
is engaged even at slow rotation (am pretty sure it is).
It sounds as if your box is set up the opposite way around to ours ie yours uses the gear ours uses for reverse (the top one), for forward? I don't know about the MS2A but my understanding is that some of the other MS2 boxes can be run with either left hand or right hand props. It would seem sensible though that the lower gear be set up as the forward one (ie a right handed prop) as it and its bearings are likely to be the better lubricated and cooled but I don't really know how important that is for component life in this box.