Gary
One tip I've seen is to connect a single cell (1.2 - 1.5v) to the motor, with an ammeter in series. Connect up the motor, U/J and prop shaft. Dollop the P38 onto the motor bed and squidge it into the hull in roughly the right place, then turn on the current. If you move the motor around, the current will increase or decrease, which indicates more or less misalignment. When the current is the lowest you've hit the optimum alignment. Let go, turn off the current and let the P38 set.
For big gaps under the motor bed e.g. in a hull with a deep keel I prefer P40, which includes chopped GRP strands.
Works for somebody - although, like Phil, I use a rigid tube to couple the two halves of the U/J while I install the running gear.
FLJ