HI MATE,
as said earlier for alignment it may be easier to use a 'silicone fuel pipe'
get one that is half the diameter inside than the shafts are, that way you would not have to make a motor mouting at exactly the right hieght and angle.
or put shaft back in and secure motor then fix it at half way on any flex felt , ie if when fitted it moves 1/4 in up and down, pack it up 1/8th in, and the same side ways.:)
with the plastic hull your only option may well be to 're-silicone it', as not much will stick to plastic and withstand the vibrations from the motor without giving way. you will need the external 'elastic' type silicone [flexable] to dampen the vibes and keep a good bond when wet.
regards
don