If I understand you right you are about to take the lower part out. If so you need to put pressure onto the pipe and not onto the shaft. Use a thick walled pipe and a plate on top of that and then place the puller bolt onto the plate leaving the shaft untouched.
Please also see thread "Bow thruster motor switch" #54459. There are some pics there and if you like I can send you more.
\Peter sy Maiken A54 #52