Prop shaft strut repairs

If original it is a SS straight piece that goes up into the hull, then two bolts are put horizontal through the holes and fiberglass mush is filled in around the whole part inside to solidify in place.  That is how they made sure it was aligned with shaft prior to fixing in place.

Often you can just drill down into the fiberglass clump until you hit the SS in a couple places and then pour Epoxy resin in the holes to fill the gaps created by the vibration of the prop over the years.  Bent, nicked or growth on blade adds to the death.  
I pour in some Acetone first to let it clean out and dry the voids.  You will probably see some run out along the strut if you drilled to the SS on the inside.  

After dry and acetone not running out bottom more, press some modeling clay or mold makers clay around the seam on the outside of the strut, then go inside and pour the resin into the drilled holes till filled.
Otherwise, cut out the clump on the inside and do over.  Make sure you are aligned again before re glassing.
Attached is a drawing from '78 that shows dimensions for the 39' Cit. Same hull, so probably same as 40'.

Change your cutlass bearing and send out the prop for checking shape and balance.