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Several things it could be.------Try this first.-------------Remove lower unit.-------------Put lower unit in nuetral.------------Put control box in nuetral.--------Re-assemble.----May have happened during waterpump work.
Are you using a remote control? Did you try disconnecting the control cable and shift it manually?
That is called a remote control. Disconnect the shift cable at the engine and put your controls in neutral and then shift the gearbox manually while spinning the prop and see if you can get it to go into reverse. Do not turn the engine over the prop should lock in both directions in reverse and in forward it should ratchet in one direction and lock in the other. If it goes into reverse put the gearbox in neutral the prop should spin free then adjust the cable to fit. Then have someone shift the control while you spin the prop and see if the controls work properly.