Are you taking the entire pump out of the boat. This would include the intake. Or are you trying to seperate the pump from the intake???
First remove the Transom Adapter. Then remove all bolts that bolt pump into intake(the part that is tuck in the bottom of the boat). Push down on the nozel or bowl and the seal between the intake and pump should break.
You shouldn't need to remove the intire pump to patch a few holes in the transom!!??