You have to pull the pump, you have to re-align it any way. The mounts compress over the years and you need to shim the engines to get it spot on.
First step,disconnect the battery and remove the engine cover completely. Spray the 3 screws that hold the hinge to the boat with WD or PB blaster, NOT the hinge to the engine cover. Do this several times in advance of pulling it. I also do it after I get th screws a little loose. Upon re installation I lather them with never seize. You can use a pencil or marker the mark the hinges, but alignment is super easy. I wedge a towel under the lip of the engine cover in the up position. I don't want to chip the gel coat. On the top of the engine cover cylinders there is a little metal C clip that is roughly 1/4" wide. you can use a super small flat screw driver to pop that out and disconnect the socket on the cylinder from the ball on the engine cover bracket
That being said. After you pull the pump, if you're doing an engine swap you will want to remove your PTO BEFORE you remove the engine, it's easier. I remove the pump and drive shaft, the remove the spark plugs. Turn the engine over so the PTO is on TDC. Looking over top of the engine from the back of the swim platform rotate the crank a little bit (1/4 revolution maybe) and stop. Then I feed some clothes line down into the spark plug hole, about 5 foot of it. Then rotate the PTO CCW. With an impeller removal tool you can use a breaker bar with a 3' cheater pipe on it and break the PTO free from the crank. It is threaded. I use an engine hoist or the like to lift the engine. You will need to remove the exhaust completely. you also have to disconnect the oil lines. I use the spark plugs (porcelain side) to plug the large oil lines. Disconnect choke cable, disconnect the oil pump cable from the PTO carb (hex nuts), remove the cable from under the carb, remove the throttle cable from under the carb on the MAG carb. Then I remove the 2 phillips screws that hold the throttle bracket to the MAG carb. This way your throttle is really damn close to where it used to be. There is a ground that bridges both engines that is from one mag cover to the other. Disconnect the voltage regulator plug, also on the mag cover. Disconnect eh stator plug right by the oil pump.Disconnect the starter lead. Disconnect the oil pump supply line, I think I jam an M8 screw in that. Disconnect the cylinder lower drain lines. I usually cut the little cable ties right next to the right angle fittings. Disconnect the fuel supply line from the filter to the pump. Disconnect the cooling lines that remain on the back of the head. Disconnect the overheat sensor plug. Remove the 3 screws that hold the engine to the mounts.
After typing all that I think I could have done it just as fast, LOL. I love working on those boats, I'm not kidding either.
Look at the throttle cable, you'll see the bracket still attached Look by the starboard front engine mount. The port side one is just below the port engine oil pump supply line filter.
Remove lower screws on the hinges
Look at the metal c clips on the struts
