Well, it's been a long time coming, but I eventually got it done as my 2009/2010 project. (2008/2009 turned out to be a full set of external and internal lights).
I used the method described above and I can confirm that it works a treat. With a bit of filing, filling and fettling, the bow thrust tubes fitted snugly in their elliptical holes. Expoxied in, then sealed inside and out with filler, then painted. (The whole hull is due for a repaint in 2010/2011 so a slight difference in colour doesn't worry me unduly).
Bath testing proved everything to be watertight and a little lightening of lead ballast soon had the tug trimmed OK. Next step is a trip to the lake for manoeuvering trials.
The thruster is a Raboesch RAB108-04 unit and is plenty powerful enough! In fact, I've got to set the TX so the thruster starts up gently and doesn't up to full power.
Thanks for the help on the fitting and for the advice on another thread re the ESC wiring colours.