I use a 45in shaft on my FTD. Any longer and it could interfere with the rod locker opening while the TM is in the stowed position.Unless you fish big water where waves would cause the TM to come out the water, no need for anything longer than the 45in shaft.
Mine came with a 45, but i switched to a 52″. The rod locker hits the motor if it is raised but there is still lots of room to get rods out. Not an issue