Try running it again with the lower end of the motor submerged in water and see if water comes out the idle relief port on the rear of the motor. If it doesn’t, the motor isn’t deep enough in the water or the copper water tube might not be inserted into the pump correctly. No water, shut it off right away and find the problem. Using an old oil drum or large garbage can full of water will ensure the motor is deep enough.
To get the water tube aligned correctly, clean off any corrosion and lightly grease it and the rubber grommet it goes in on top of the water pump. You might want to have someone give you a hand when reinstalling the gearcase as three things have to be aligned correctly before tightening the bolts. They would be the driveshaft splines, the shift rod, and the water tube. Quite often I hold a small flashlight in my teeth so I can see the water tube aligning correctly with the pump. Sometimes a wire hook is needed to do this. Bright colored nail polish will help to get the shift rod aligned correctly.
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