Yank the bolts holding the transom adapter. Than, use some wire to cut through any silicone holding it on. Next I would onbolt the suction housing from the intake adapter and yank the whole pump out the back. NOTE-pull the hand hole cover before pulling the last bolt out of the intake, you can grab the sahft through there when you pull it out the back of the boat.
Next is the intake. Are you having it machined for a shoe and ride plate? If not, leave it in there, unless it leaks. Then you should pull it out and add a shoe and ride plate before you put it in.