6) Are there other repairs I should be expecting soon?
>> If the motor is new or rebuilt and has not been running, you will have some 'bugs' to work out once the boat gets into the water. Things like guages and electronics. I hope they put on new parts like starter, belt, hoses, impeller, etc.

Do most people replace the transmission when they replace the motor?
>> No. Change the fluids and take it for a test run to see how smooth/rough it operates.