I'm really not sure it'll come out the top due to the size of the hole, and the crane is going to be very unstable with engine and box high enough to clear the front cross member.
Put the car on your tallest axle stands and take it out the bottom on a sling. The weight is too eccentric to safely balance engine and box on a jack, and the sump isn't strong enough to take the point load on a jack anyway so use a sling at either end.
When it's on the floor either roll the car on its rear wheels out of the way, or even put the whole engine/box assembly on the front legs of your crane, using some 6x2s or scaffold boards to spread the load. Which of these strategies you use will depend on your workspace / the height of your axle stands etc.
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