I did that on a clients boat when he could'nt locate a drop center tranny. The stern tube was removed and the engine, replacement tranny and shaft reoriented to the desired angle. The motor mount mounting plates were remounted to match new engine angle. The shaft was immobilized to keep it from moving out of position. The stern tube was covered with packing tape to avoid epoxy from sticking to it. . To make sure the shaft did not stick to the epoxy and to make sliding out easier, I wrapped foam around the shaft and covered that with packing tape.
A glob of epoxy putty was placed on the stern tube and the tube pushed against the dead wood and fixed to not move. Excess squeezed out putty is cleaned off and shaped. The epoxy putty was made with WEST High Density filler.
After the epoxy cured, stern tube and shaft was removed and the shaft hole enlarged in the epoxy wedge, cleaned up and any voids in the epoxy filled. Another epoxy wedge with the same angle as the one made on the outside is made in a mold and glued into the inside of the hulls deadwood to insure the bolts, washers and nuts on the inside were perpendicular to the inside face of the deadwood and parallel to the face of the new wedge on the outside.
The stern tube is slid back onto the shaft, holes for fastners drilled and stern tube installed with Life Caulk. The engine is checked for alignment and mounts adjusted if necessary.
The angle of the shaft did not change a lot so the epoxy wedge was 1/2" at the thick end. If a thicker wedge was required because of a greater shaft angle change, I might reinforce the wedge with fabric.
The top front of the engine touched the underside of the floor after reangling. I routed a recess in the plywood to clear the engine.
Also, the shaft on this boat was short and thick so there was no shaft droop. With longer shafts, a more careful alignment of the shaft prior to creating the wedge is advised.
Replacing the cutlass bearing with the stern tube off the boat is so much easier than on the boat so that is recommended. I use a press.